Joshua B Plotkin, Phd

faculty photo

Contact information
Professor of Biology
Lynch Labs room 219
433 S. University Ave
Philadelphia, PA 19104
AB (scl)
Harvard College, 1999.
Princeton University, 2003.
Harvard Society of Fellows, 2007.
Permanent link
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Description of Research Expertise

Molecular evolution, Population genetics, Mathematical biology


Board of Reviewing Editors, Science (AAAS)
Editorial Board, Cell Reports

Selected Publications

  • Newberry MG, Ahern C, Clark R, Plotkin JB. Detecting evolutionary forces in language change. Nature (in press)
  • Stewart A, Parsons T, Plotkin JB. Evolutionary consequences of behavioral diversity. PNAS 113: 7003-7009 (2016)
  • Nourmohammad A, Otwinowski J, Plotkin JB. Host-pathogen co-evolution and the emergence of broadly neutralizing antibodies in chronic infections. PLOS Genetics 12: 1006171 (2016)
  • Shah P, McCandlish M, Plotkin JB. Contingency and entrenchment in protein evolution under purifying selection. PNAS 112:3226–3235 (2015) [pdf]
  • Stewart A, Plotkin JB. The collapse of cooperation in evolving games. PNAS 111: 17558-17563 (2014) [pdf]
  • Otwinowski J, Plotkin JB. Inferring fitness landscapes by regression produces biased estimates of epistasis. PNAS 111: 2301-2309 (2014) [pdf]
  • Shah P, Ding Y, Niemczyk M, Kudla G, Plotkin JB. Rate-limiting steps in yeast protein translation. Cell 153: 1589-1601 (2013) [[pdf]
  • Stewart AJ, Plotkin JB. From extortion to generosity, evolution in the Iterated Prisoner's Dilemma. PNAS 110: 15348-15353 (2013) [pdf]
  • McCandlish D, Rajon E, Shah P, Ding Y, Plotkin JB. The role of epistasis in protein evolution. Nature 497: E1–E2 (2013) [pdf]
  • Stewart AJ, Plotkin JB. Extortion and cooperation in the Prisoner's Dilemma. PNAS 109:10134-10135. (2012) [pdf]
  • Lipsitch M, Plotkin JB, Simonsen L, Bloom B. Evolution, safety, and highly pathogenic influenza viruses. Science 336:1529-153 (2012) [pdf]
  • Morlon H, Parsons T, Plotkin JB. Reconciling molecular phylogenies with the fossil record. PNAS 108: 16327-16332 (2011) [pdf] [cover]
  • Kryazhimskiy S, Draghi J, Plotkin JB. In evolution, the sum is less than its parts. Science 332: 1160-1161 (2011) [pdf]
  • Der R, Epstein C, Plotkin JB. The dynamics of neutral and selected alleles when the offspring distribution is skewed. Genetics 191: 1331-1344 (2012) [pdf]
  • Kryazhimskiy S, Dushoff J, Bazykin G, Plotkin JB. Prevalence of epistasis in the evolution of influenza A surface proteins. PLoS Genetics 7: 1001301 (2011) [pdf]
  • Plotkin JB, Kudla G. Synonymous but not the same: the causes and consequences of codon bias. Nature Reviews Genetics 12: 32-42 (2011) [pdf]
  • Draghi J, Parsons TL, Wagner G, Plotkin JB. Mutational robustness can facilitate adaptation. Nature 426: 353-355 (2010) [pdf]
  • Morlon H, Potts M, Plotkin JB. Inferring the dynamics of diversification: a coalescent approach. PLoS Biology 8: 1000493 (2010) [pdf]
  • Kudla G, Murray AW, Tollervey D, Plotkin JB. Coding-sequence determinants of gene expression in Escherichia coli. Science 324:255-258 (2009) [pdf]
  • Kryazhimskiy S, Tkacik G, Plotkin JB. The dynamics of adaptation on correlated fitness landscapes. PNAS 106: 18638-18643 (2009) [pdf]
  • Goldstein E, Dushoff J, Ma J, Plotkin JB, Earn DJ, Lipsitch M. Reconstructing influenza incidence by deconvolution of daily mortality time series. PNAS 106: 21825–21829 (2009) [pdf]
  • Kryazhimskiy S, Plotkin JB. The population genetics of dN/dS. PLoS Genetics 4: 1000304 (2008) [pdf]
  • Dushoff J, Plotkin JB, Levin SA, Earn DE. Dynamic resonance can explain the seasonality of influenza incidence. PNAS 101: 16915-16916 (2004) [pdf]
  • Plotkin JB, Dushoff J, Fraser HB. Detecting selection using a single genome sequence of M. tuberculosis and P. falciparum. Nature 428: 942-945 (2004) [pdf]
  • Plotkin JB, Robins H, Levine A. Tissue specific codon usage and the expression of human genes. PNAS 101: 12588-12591 (2004) [pdf]
  • Plotkin JB, Dushoff J. Codon bias and frequency-dependent selection on the hemagglutinin epitopes of Influenza A virus. PNAS 100: 7152-7157 (2003) [pdf]
  • Plotkin JB, Dushoff J, Levin SA. Hemagglutinin sequence clusters and the antigenic evolution of Influenza A virus. PNAS 99: 6263-6268 (2002) [pdf]
  • Krakauer D, Plotkin JB. Redundancy, anti-redundancy, and the stability of genomes. PNAS 99: 1405-1409 (2002) [pdf]
  • Plotkin JB, Potts M, Yu D, Bunyavejchewin S, Condit R, Foster R, Hubbell S, LaFrankie J, Manokaran N, Seng L, Sukumar R, Nowak MA, Ashton PS. Predicting species diversity in tropical forests. PNAS 97:10850-10854 (2000) [pdf]
  • Nowak M, Plotkin JB, Jansen V. The evolution of syntactic communication. Nature 404: 495-498 (2000) [pdf]

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Last updated: 10/03/2017
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