Joshua B. Plotkin

Associate Professor of Biology (SAS), Computer and Information Science (SEAS)
219 Carolyn Lynch Laboratories
jplotkin@sasDOTupennDOTedu
Research Interests: 

I use mathematics and computation to study questions in evolutionary biology and ecology. My research is concerned primarily with the origin and maintenance of genetic variation within populations (read more).

Education:
Junior Fellow, Harvard Society of Fellows, 2007
PhD, Princeton University, 2007
AB scl, Harvard College, 1999

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

Selected Publications:

Stewart A, Plotkin JB. From extortion to generosity, evolution in the Iterated Prisoner's Dilemma. PNAS 110: 15348-15353 (2013) [pdf]

Shah P, Ding Y, Niemczyk M, Kudla G, Plotkin JB. Rate-limiting steps in yeast protein translation. Cell 153:1589-1601 (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]

Morlon H, Parsons T, Plotkin JB. Reconciling molecular phylogenies with the fossil record. PNAS 108: 16327–16332 (2012) [pdf][cover]

Lipsitch M, Plotkin JB, Simonsen L, Bloom B. Evolution, safety, and highly pathogenic influenza viruses. Science 336:1529-153 (2012)  [pdf]

Der R, Epstein C, Plotkin JB. Generalized population models and the nature of genetic drift. Theoretical Population Biology 80: 80–98 (2011) [pdf]

Kryazhimskiy S, Draghi J, Plotkin JB. In evolution, the sum is less than its parts. Science 332: 1160-1161 (2011) [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 T, 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. Dynamical resonance can explain the seasonality of influenza incidence. PNAS 101: 16915-16916 (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, Fraser HB. Detecting selection using a single genome sequence of M. tuberculosis and P. falciparum. Nature 428: 942-945 (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]

Google Scholar