Joshua Plotkin, Ph.D.

Assistant Professor, Department of Biology

Office Address:
219 Lynch Building
433 S. University Ave.
Philadelphia, PA 19104

Telephone: 215-573-8052
Fax:  TBA
jplotkin@sas.upenn.edu


Lab Website

RESEARCH SUMMARY

I am broadly interested in molecular population genetics and evolution. My research is based mostly on mathematical modeling and computation. One primary goal is to develop statistical methods for inferring the action of natural selection from intra-specific polymorphism data and from inter-specific sequence variation.

Of particular interest are applications to the genomes of pathogens, whose proteins experience a wide range of selective pressures influenced by interactions with their hosts.

I also investigate an array of topics in evolutionary theory – such as the evolution of mutation rates, the evolution of robustness to environmental and mutational perturbation, somatic evolution, the structure of epistasis across a genome, and the determinates of protein evolutionary rates.

Specific research projects include:

• analysis of protein evolution and synonymous evolution in RNA viruses and phages
• mathematical models of influenza evolution and epidemiology
• time series analysis of pneumonia and influenza deaths
• computational methods to detect epistatic loci
• computational studies on the effects of codon usage for transcription and translation
• in silico studies on the fitness landscapes of RNA secondary structures
• mathematical models for the evolution of robustness and cancer
  

Selected Publications:
Plotkin JB, Dushoff J, Desai MM, Fraser HB. Codon usage and selection on proteins. J. Mol. Evol. 63:635-657 (2006)

Plotkin JB, Dushoff J, Desai MM, Fraser HB. Estimating selection pressures from limited comparative data. Mol. Biol. Evol. 23:1457-1459 (2006)

HB Fraser, P Khaitovich, JB Plotkin, S Paabo, MB Eisen. Aging and gene expression in the primate brain. PloS Biology 9:274 (2005)

Dushoff J, Plotkin JB, Levin SA, Earn DE. Dynamic resonance can explain the seasonality of influenza incidence. Proceedings of the National Academy of Sciences, 101: 16915–16916 (2004)

Plotkin JB, Robins H, Levine A. Tissue specific codon usage and the expression of human genes. Proceedings of the National Academy of Sciences 101:12588-12591 (2004)

Plotkin JB, Dushoff J, Fraser HB. Detecting selection using a single genome sequence of M. tuberculosis and P. falciparum. Nature 428: 942-945 (2004).

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 100: 7152-7157 (2003).

Plotkin JB, Dushoff J, Levin SA. Hemagglutinin sequence clusters and the antigenic evolution of Influenza A virus. Proceedings of the National Academy of Sciences 99: 6263-6268 (2002.)

Plotkin JB, Nowak MA. The different effects of apoptosis and DNA repair on tumorigenesis. Journal of Theoretical Biology 214: 453-467 (2002).

Krakauer D, Plotkin JB. Redundancy, anti-redundancy, and the stability of genomes. Proceedings of the National Academy of Sciences 99: 1405-1409 (2002).

RECENT PUBLICATIONS