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Department of Biology People
 

Joshua B. Plotkin

Associate Professor of Biology (SAS), Computer and Information Science (SEAS)

219 Carolyn Lynch Laboratories
Department of Biology
University of Pennsylvania
Philadelphia, PA 19104 USA


E:

jplotkin AT sas DOT upenn DOT edu

Plotkin Lab Website


research
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, 2003
AB (scl), Harvard College, 1999

service
Board of Reviewing Editors, Science (AAAS)
Editorial Board, Cell Reports
Associate Editor, Journal of Molecular Evolution


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

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. Dynamic 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]

Pubmed Articles



People
Department of Biology
School of Arts and Sciences
University of Pennsylvania

last updated October 14, 2011