Joshua B. Plotkin - Publications

Affiliations: 
University of Pennsylvania, Philadelphia, PA, United States 
Area:
Evolutionary biology

93 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2024 Morsky B, Plotkin JB, Akçay E. Convergence of reputations under indirect reciprocity. Journal of Theoretical Biology. 595: 111947. PMID 39304120 DOI: 10.1016/j.jtbi.2024.111947  0.605
2024 Kawakatsu M, Kessinger TA, Plotkin JB. A mechanistic model of gossip, reputations, and cooperation. Proceedings of the National Academy of Sciences of the United States of America. 121: e2400689121. PMID 38717858 DOI: 10.1073/pnas.2400689121  0.773
2024 Morsky B, Plotkin JB, Akçay E. Indirect reciprocity with Bayesian reasoning and biases. Plos Computational Biology. 20: e1011979. PMID 38662682 DOI: 10.1371/journal.pcbi.1011979  0.6
2024 Kawakatsu M, Michel-Mata S, Kessinger TA, Tarnita CE, Plotkin JB. When do stereotypes undermine indirect reciprocity? Plos Computational Biology. 20: e1011862. PMID 38427626 DOI: 10.1371/journal.pcbi.1011862  0.772
2023 Schrom E, Kinzig A, Forrest S, Graham AL, Levin SA, Bergstrom CT, Castillo-Chavez C, Collins JP, de Boer RJ, Doupé A, Ensafi R, Feldman S, Grenfell BT, Halderman JA, Huijben S, ... ... Plotkin J, et al. Challenges in cybersecurity: Lessons from biological defense systems. Mathematical Biosciences. 109024. PMID 37270102 DOI: 10.1016/j.mbs.2023.109024  0.749
2023 Cooney DB, Levin SA, Mori Y, Plotkin JB. Evolutionary dynamics within and among competing groups. Proceedings of the National Academy of Sciences of the United States of America. 120: e2216186120. PMID 37155901 DOI: 10.1073/pnas.2216186120  0.581
2020 Tilman AR, Plotkin JB, Akçay E. Evolutionary games with environmental feedbacks. Nature Communications. 11: 915. PMID 32060275 DOI: 10.1038/S41467-020-14531-6  0.761
2019 Radzvilavicius AL, Stewart AJ, Plotkin JB. Evolution of empathetic moral evaluation. Elife. 8. PMID 30964002 DOI: 10.7554/Elife.44269  0.302
2019 Carja O, Plotkin JB. Evolutionary Rescue Through Partly Heritable Phenotypic Variability. Genetics. PMID 30696715 DOI: 10.1534/Genetics.118.301758  0.399
2018 Posfai A, Zhou J, Plotkin JB, Kinney JB, McCandlish DM. Selection for Protein Stability Enriches for Epistatic Interactions. Genes. 9. PMID 30134605 DOI: 10.3390/Genes9090423  0.319
2018 Mittal P, Brindle J, Stephen J, Plotkin JB, Kudla G. Codon usage influences fitness through RNA toxicity. Proceedings of the National Academy of Sciences of the United States of America. PMID 30082392 DOI: 10.1073/Pnas.1810022115  0.312
2018 Otwinowski J, McCandlish DM, Plotkin JB. Inferring the shape of global epistasis. Proceedings of the National Academy of Sciences of the United States of America. 115: E7550-E7558. PMID 30037990 DOI: 10.1073/Pnas.1804015115  0.336
2017 Gulisija D, Plotkin JB. Phenotypic plasticity promotes recombination and gene clustering in periodic environments. Nature Communications. 8: 2041. PMID 29229921 DOI: 10.1038/S41467-017-01952-Z  0.791
2017 Newberry MG, Ahern CA, Clark R, Plotkin JB. Detecting evolutionary forces in language change. Nature. PMID 29088703 DOI: 10.1038/Nature24455  0.321
2017 Carja O, Xing T, Wallace EWJ, Plotkin JB, Shah P. riboviz: analysis and visualization of ribosome profiling datasets. Bmc Bioinformatics. 18: 461. PMID 29070028 DOI: 10.1186/S12859-017-1873-8  0.758
2017 Plotkin JB. Molecular evolution: No escape from the tangled bank. Nature. PMID 29045393 DOI: 10.1038/Nature24152  0.379
2017 Carja O, Plotkin JB. The evolutionary advantage of heritable phenotypic heterogeneity. Scientific Reports. 7: 5090. PMID 28698577 DOI: 10.1038/S41598-017-05214-2  0.351
2016 Stewart AJ, Parsons TL, Plotkin JB. Evolutionary consequences of behavioral diversity. Proceedings of the National Academy of Sciences of the United States of America. PMID 27791109 DOI: 10.1073/Pnas.1608990113  0.357
2016 Newberry MG, McCandlish DM, Plotkin JB. Assortative mating can impede or facilitate fixation of underdominant alleles. Theoretical Population Biology. PMID 27497738 DOI: 10.1016/J.Tpb.2016.07.003  0.37
2016 Nourmohammad A, Otwinowski J, Plotkin JB. Host-Pathogen Coevolution and the Emergence of Broadly Neutralizing Antibodies in Chronic Infections. Plos Genetics. 12: e1006171. PMID 27442127 DOI: 10.1371/Journal.Pgen.1006171  0.321
2016 McCandlish DM, Shah P, Plotkin JB. Epistasis and the Dynamics of Reversion in Molecular Evolution. Genetics. PMID 27194749 DOI: 10.1534/Genetics.116.188961  0.535
2016 McCandlish DM, Plotkin JB. Transcriptional errors and the drift barrier. Proceedings of the National Academy of Sciences of the United States of America. PMID 26966235 DOI: 10.1073/Pnas.1601785113  0.375
2016 Weinberg DE, Shah P, Eichhorn SW, Hussmann JA, Plotkin JB, Bartel DP. Improved Ribosome-Footprint and mRNA Measurements Provide Insights into Dynamics and Regulation of Yeast Translation. Cell Reports. PMID 26876183 DOI: 10.1016/J.Celrep.2016.01.043  0.496
2016 Gulisija D, Kim Y, Plotkin JB. Phenotypic Plasticity Promotes Balanced Polymorphism in Periodic Environments by a Genomic Storage Effect. Genetics. PMID 26857626 DOI: 10.1534/Genetics.115.185702  0.788
2015 Neverov AD, Kryazhimskiy S, Plotkin JB, Bazykin GA. Coordinated Evolution of Influenza A Surface Proteins. Plos Genetics. 11: e1005404. PMID 26247472 DOI: 10.1371/Journal.Pgen.1005404  0.784
2015 McCandlish DM, Otwinowski J, Plotkin JB. Detecting epistasis from an ensemble of adapting populations. Evolution; International Journal of Organic Evolution. PMID 26194030 DOI: 10.1111/Evo.12735  0.405
2015 Shah P, McCandlish DM, Plotkin JB. Contingency and entrenchment in protein evolution under purifying selection. Proceedings of the National Academy of Sciences of the United States of America. 112: E3226-35. PMID 26056312 DOI: 10.1073/Pnas.1412933112  0.58
2015 Schulte MB, Draghi JA, Plotkin JB, Andino R. Experimentally guided models reveal replication principles that shape the mutation distribution of RNA viruses. Elife. 4. PMID 25635405 DOI: 10.7554/Elife.03753  0.337
2015 McCandlish DM, Epstein CL, Plotkin JB. Formal properties of the probability of fixation: identities, inequalities and approximations. Theoretical Population Biology. 99: 98-113. PMID 25450112 DOI: 10.1016/J.Tpb.2014.11.004  0.376
2015 Stewart AJ, Plotkin JB. The evolvability of cooperation under local and non-local mutations Games. 6: 231-250. DOI: 10.3390/G6030231  0.393
2014 Stewart AJ, Plotkin JB. Collapse of cooperation in evolving games. Proceedings of the National Academy of Sciences of the United States of America. 111: 17558-63. PMID 25422421 DOI: 10.1073/Pnas.1408618111  0.373
2014 Otwinowski J, Plotkin JB. Inferring fitness landscapes by regression produces biased estimates of epistasis. Proceedings of the National Academy of Sciences of the United States of America. 111: E2301-9. PMID 24843135 DOI: 10.1073/Pnas.1400849111  0.381
2014 Der R, Plotkin JB. The equilibrium allele frequency distribution for a population with reproductive skew. Genetics. 196: 1199-216. PMID 24473932 DOI: 10.1534/Genetics.114.161422  0.789
2014 McCandlish DM, Epstein CL, Plotkin JB. The inevitability of unconditionally deleterious substitutions during adaptation. Evolution; International Journal of Organic Evolution. 68: 1351-64. PMID 24410330 DOI: 10.1111/Evo.12350  0.374
2014 Feder AF, Kryazhimskiy S, Plotkin JB. Identifying signatures of selection in genetic time series. Genetics. 196: 509-22. PMID 24318534 DOI: 10.1534/Genetics.113.158220  0.794
2013 Draghi JA, Plotkin JB. Selection biases the prevalence and type of epistasis along adaptive trajectories. Evolution; International Journal of Organic Evolution. 67: 3120-31. PMID 24151997 DOI: 10.1111/Evo.12192  0.413
2013 Stewart AJ, Plotkin JB. From extortion to generosity, evolution in the Iterated Prisoner's Dilemma. Proceedings of the National Academy of Sciences of the United States of America. 110: 15348-53. PMID 24003115 DOI: 10.1073/Pnas.1306246110  0.346
2013 Rajon E, Plotkin JB. The evolution of genetic architectures underlying quantitative traits. Proceedings. Biological Sciences / the Royal Society. 280: 20131552. PMID 23986107 DOI: 10.1098/Rspb.2013.1552  0.342
2013 Stewart AJ, Plotkin JB. The evolution of complex gene regulation by low-specificity binding sites. Proceedings. Biological Sciences / the Royal Society. 280: 20131313. PMID 23945682 DOI: 10.1098/Rspb.2013.1313  0.307
2013 Li Y, Bostick DL, Sullivan CB, Myers JL, Griesemer SB, Stgeorge K, Plotkin JB, Hensley SE. Single hemagglutinin mutations that alter both antigenicity and receptor binding avidity influence influenza virus antigenic clustering. Journal of Virology. 87: 9904-10. PMID 23824816 DOI: 10.1128/Jvi.01023-13  0.301
2013 Shah P, Ding Y, Niemczyk M, Kudla G, Plotkin JB. Rate-limiting steps in yeast protein translation. Cell. 153: 1589-601. PMID 23791185 DOI: 10.1016/J.Cell.2013.05.049  0.5
2013 McCandlish DM, Rajon E, Shah P, Ding Y, Plotkin JB. The role of epistasis in protein evolution. Nature. 497: E1-2; discussion E2-. PMID 23719465 DOI: 10.1038/Nature12219  0.535
2012 Ding Y, Shah P, Plotkin JB. Weak 5'-mRNA secondary structures in short eukaryotic genes. Genome Biology and Evolution. 4: 1046-53. PMID 23034215 DOI: 10.1093/Gbe/Evs082  0.489
2012 Stewart AJ, Seymour RM, Pomiankowski A, Plotkin JB. The population genetics of cooperative gene regulation. Bmc Evolutionary Biology. 12: 173. PMID 22954408 DOI: 10.1186/1471-2148-12-173  0.319
2012 Morlon H, Kemps BD, Plotkin JB, Brisson D. Explosive radiation of a bacterial species group. Evolution; International Journal of Organic Evolution. 66: 2577-86. PMID 22834754 DOI: 10.1111/J.1558-5646.2012.01598.X  0.622
2012 Lipsitch M, Plotkin JB, Simonsen L, Bloom B. Evolution, safety, and highly pathogenic influenza viruses. Science (New York, N.Y.). 336: 1529-31. PMID 22723411 DOI: 10.1126/Science.1223204  0.351
2012 Stewart AJ, Plotkin JB. Extortion and cooperation in the Prisoner's Dilemma. Proceedings of the National Academy of Sciences of the United States of America. 109: 10134-5. PMID 22711812 DOI: 10.1073/Pnas.1208087109  0.305
2012 Der R, Epstein C, Plotkin JB. Dynamics of neutral and selected alleles when the offspring distribution is skewed. Genetics. 191: 1331-44. PMID 22661323 DOI: 10.1534/Genetics.112.140038  0.798
2012 Stewart AJ, Parsons TL, Plotkin JB. Environmental robustness and the adaptability of populations. Evolution; International Journal of Organic Evolution. 66: 1598-612. PMID 22519793 DOI: 10.1111/J.1558-5646.2011.01526.X  0.348
2012 Desai MM, Nicolaisen LE, Walczak AM, Plotkin JB. The structure of allelic diversity in the presence of purifying selection. Theoretical Population Biology. 81: 144-57. PMID 22198521 DOI: 10.1016/J.Tpb.2011.12.002  0.606
2012 Walczak AM, Nicolaisen LE, Plotkin JB, Desai MM. The structure of genealogies in the presence of purifying selection: a fitness-class coalescent. Genetics. 190: 753-79. PMID 22135349 DOI: 10.1534/Genetics.111.134544  0.601
2012 Draghi JA, Plotkin JB. A network of paths toward innovation Bioessays. DOI: 10.1002/Bies.201200016  0.389
2011 Morlon H, Parsons TL, Plotkin JB. Reconciling molecular phylogenies with the fossil record. Proceedings of the National Academy of Sciences of the United States of America. 108: 16327-32. PMID 21930899 DOI: 10.1073/Pnas.1102543108  0.632
2011 Der R, Epstein CL, Plotkin JB. Generalized population models and the nature of genetic drift. Theoretical Population Biology. 80: 80-99. PMID 21718713 DOI: 10.1016/J.Tpb.2011.06.004  0.793
2011 Draghi JA, Plotkin JB. Molecular evolution: Hidden diversity sparks adaptation. Nature. 474: 45-6. PMID 21637251 DOI: 10.1038/474045A  0.385
2011 Kryazhimskiy S, Draghi JA, Plotkin JB. Evolution. In evolution, the sum is less than its parts. Science (New York, N.Y.). 332: 1160-1. PMID 21636764 DOI: 10.1126/Science.1208072  0.774
2011 Vishnoi A, Sethupathy P, Simola D, Plotkin JB, Hannenhalli S. Genome-wide survey of natural selection on functional, structural, and network properties of polymorphic sites in Saccharomyces paradoxus. Molecular Biology and Evolution. 28: 2615-27. PMID 21478372 DOI: 10.1093/Molbev/Msr085  0.402
2011 Kryazhimskiy S, Dushoff J, Bazykin GA, Plotkin JB. Prevalence of epistasis in the evolution of influenza A surface proteins. Plos Genetics. 7: e1001301. PMID 21390205 DOI: 10.1371/Journal.Pgen.1001301  0.778
2011 Draghi JA, Parsons TL, Plotkin JB. Epistasis increases the rate of conditionally neutral substitution in an adapting population. Genetics. 187: 1139-52. PMID 21288876 DOI: 10.1534/Genetics.110.125997  0.406
2011 Plotkin JB, Kudla G. Synonymous but not the same: the causes and consequences of codon bias. Nature Reviews. Genetics. 12: 32-42. PMID 21102527 DOI: 10.1038/Nrg2899  0.39
2010 Morlon H, Potts MD, Plotkin JB. Inferring the dynamics of diversification: a coalescent approach. Plos Biology. 8. PMID 20927410 DOI: 10.1371/Journal.Pbio.1000493  0.753
2010 Vishnoi A, Kryazhimskiy S, Bazykin GA, Hannenhalli S, Plotkin JB. Young proteins experience more variable selection pressures than old proteins. Genome Research. 20: 1574-81. PMID 20921233 DOI: 10.1101/Gr.109595.110  0.772
2010 Parsons TL, Quince C, Plotkin JB. Some consequences of demographic stochasticity in population genetics. Genetics. 185: 1345-54. PMID 20457879 DOI: 10.1534/Genetics.110.115030  0.382
2010 Draghi JA, Parsons TL, Wagner GP, Plotkin JB. Mutational robustness can facilitate adaptation. Nature. 463: 353-5. PMID 20090752 DOI: 10.1038/Nature08694  0.412
2009 Goldstein E, Dushoff J, Ma J, Plotkin JB, Earn DJ, Lipsitch M. Reconstructing influenza incidence by deconvolution of daily mortality time series. Proceedings of the National Academy of Sciences of the United States of America. 106: 21825-9. PMID 20080801 DOI: 10.1073/Pnas.0902958106  0.768
2009 Kryazhimskiy S, Tkacik G, Plotkin JB. The dynamics of adaptation on correlated fitness landscapes. Proceedings of the National Academy of Sciences of the United States of America. 106: 18638-43. PMID 19858497 DOI: 10.1073/Pnas.0905497106  0.799
2009 Ndifon W, Plotkin JB, Dushoff J. On the accessibility of adaptive phenotypes of a bacterial metabolic network. Plos Computational Biology. 5: e1000472. PMID 19696877 DOI: 10.1371/Journal.Pcbi.1000472  0.772
2009 Roy S, Vandenberghe LH, Kryazhimskiy S, Grant R, Calcedo R, Yuan X, Keough M, Sandhu A, Wang Q, Medina-Jaszek CA, Plotkin JB, Wilson JM. Isolation and characterization of adenoviruses persistently shed from the gastrointestinal tract of non-human primates. Plos Pathogens. 5: e1000503. PMID 19578438 DOI: 10.1371/Journal.Ppat.1000503  0.768
2008 Kryazhimskiy S, Plotkin JB. The population genetics of dN/dS. Plos Genetics. 4: e1000304. PMID 19081788 DOI: 10.1371/Journal.Pgen.1000304  0.795
2008 Desai MM, Plotkin JB. The polymorphism frequency spectrum of finitely many sites under selection. Genetics. 180: 2175-91. PMID 18854590 DOI: 10.1534/Genetics.108.087361  0.596
2008 Parsons TL, Quince C, Plotkin JB. Absorption and fixation times for neutral and quasi-neutral populations with density dependence. Theoretical Population Biology. 74: 302-10. PMID 18835288 DOI: 10.1016/J.Tpb.2008.09.001  0.357
2008 Sethupathy P, Giang H, Plotkin JB, Hannenhalli S. Genome-wide analysis of natural selection on human cis-elements. Plos One. 3: e3137. PMID 18781197 DOI: 10.1371/Journal.Pone.0003137  0.338
2008 Kryazhimskiy S, Bazykin GA, Plotkin JB, Plotkin J, Dushoff J. Directionality in the evolution of influenza A haemagglutinin. Proceedings. Biological Sciences / the Royal Society. 275: 2455-64. PMID 18647721 DOI: 10.1098/Rspb.2008.0521  0.771
2008 Lucks JB, Nelson DR, Kudla GR, Plotkin JB. Genome landscapes and bacteriophage codon usage. Plos Computational Biology. 4: e1000001. PMID 18463708 DOI: 10.1371/Journal.Pcbi.1000001  0.348
2007 Fraser HB, Plotkin JB. Using protein complexes to predict phenotypic effects of gene mutation. Genome Biology. 8: R252. PMID 18042286 DOI: 10.1186/Gb-2007-8-11-R252  0.318
2007 Green JL, Plotkin JB. A statistical theory for sampling species abundances. Ecology Letters. 10: 1037-45. PMID 17803677 DOI: 10.1111/J.1461-0248.2007.01101.X  0.496
2007 Dushoff J, Plotkin JB, Viboud C, Simonsen L, Miller M, Loeb M, Earn DJ. Vaccinating to protect a vulnerable subpopulation. Plos Medicine. 4: e174. PMID 17518515 DOI: 10.1371/Journal.Pmed.0040174  0.746
2007 Plotkin JB, Fraser HB. Assessing the determinants of evolutionary rates in the presence of noise. Molecular Biology and Evolution. 24: 1113-21. PMID 17347158 DOI: 10.1093/Molbev/Msm044  0.315
2006 Plotkin JB, Dushoff J, Desai MM, Fraser HB. Codon usage and selection on proteins. Journal of Molecular Evolution. 63: 635-53. PMID 17043750 DOI: 10.1007/S00239-005-0233-X  0.727
2006 Plotkin JB, Dushoff J, Desai MM, Fraser HB. Estimating selection pressures from limited comparative data. Molecular Biology and Evolution. 23: 1457-9. PMID 16754640 DOI: 10.1093/Molbev/Msl021  0.686
2006 Dushoff J, Plotkin JB, Viboud C, Earn DJ, Simonsen L. Mortality due to influenza in the United States--an annualized regression approach using multiple-cause mortality data. American Journal of Epidemiology. 163: 181-7. PMID 16319291 DOI: 10.1093/Aje/Kwj024  0.743
2005 Lukhtanov VA, Kandul NP, Plotkin JB, Dantchenko AV, Haig D, Pierce NE. Reinforcement of pre-zygotic isolation and karyotype evolution in Agrodiaetus butterflies. Nature. 436: 385-9. PMID 16034417 DOI: 10.1038/Nature03704  0.356
2004 Dushoff J, Plotkin JB, Levin SA, Earn DJ. Dynamical resonance can account for seasonality of influenza epidemics. Proceedings of the National Academy of Sciences of the United States of America. 101: 16915-6. PMID 15557003 DOI: 10.1073/Pnas.0407293101  0.769
2004 Plotkin JB, Dushoff J, Fraser HB. Detecting selection using a single genome sequence of M. tuberculosis and P. falciparum. Nature. 428: 942-5. PMID 15118727 DOI: 10.1038/Nature02458  0.601
2004 Levin SA, Dushoff J, Plotkin JB. Evolution and persistence of influenza A and other diseases. Mathematical Biosciences. 188: 17-28. PMID 14766091 DOI: 10.1016/J.Mbs.2003.08.010  0.73
2003 Plotkin JB, Dushoff J. Codon bias and frequency-dependent selection on the hemagglutinin epitopes of influenza A virus. Proceedings of the National Academy of Sciences of the United States of America. 100: 7152-7. PMID 12748378 DOI: 10.1073/Pnas.1132114100  0.637
2002 Plotkin JB, Chave J, Ashton PS. Cluster analysis of spatial patterns in Malaysian tree species. The American Naturalist. 160: 629-44. PMID 18707513 DOI: 10.1086/342823  0.577
2002 Plotkin JB, Dushoff J, Levin SA. Hemagglutinin sequence clusters and the antigenic evolution of influenza A virus. Proceedings of the National Academy of Sciences of the United States of America. 99: 6263-8. PMID 11972025 DOI: 10.1073/Pnas.082110799  0.713
2002 Krakauer DC, Plotkin JB. Redundancy, antiredundancy, and the robustness of genomes. Proceedings of the National Academy of Sciences of the United States of America. 99: 1405-9. PMID 11818563 DOI: 10.1073/Pnas.032668599  0.371
2002 Plotkin JB, Muller-Landau HC. Sampling the species composition of a landscape Ecology. 83: 3344-3356. DOI: 10.1890/0012-9658(2002)083[3344:Stscoa]2.0.Co;2  0.587
2002 Potts MD, Ashton PS, Kaufman LS, Plotkin JB. Habitat patterns in tropical rain forests: A comparison of 105 plots in northwest Borneo Ecology. 83: 2782-2797. DOI: 10.1890/0012-9658(2002)083[2782:Hpitrf]2.0.Co;2  0.616
2000 Plotkin JB, Potts MD, Leslie N, Manokaran N, Lafrankie J, Ashton PS. Species-area curves, spatial aggregation, and habitat specialization in tropical forests. Journal of Theoretical Biology. 207: 81-99. PMID 11027481 DOI: 10.1006/Jtbi.2000.2158  0.608
2000 Plotkin JB, Potts MD, Yu DW, Bunyavejchewin S, Condit R, Foster R, Hubbell S, LaFrankie J, Manokaran N, Seng LH, Sukumar R, Nowak MA, Ashton PS. Predicting species diversity in tropical forests. Proceedings of the National Academy of Sciences of the United States of America. 97: 10850-4. PMID 11005859 DOI: 10.1073/Pnas.97.20.10850  0.608
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