Dr. Robin M. Bush

Ecology and Evolutionary Biology
5207 McGaugh
University of California
Irvine, CA 92697


students: please contact me using the EEE message board for your class
non-students: rmbush at uci.edu
phone: 949-824-2243
fax: 949-824-2181

Note to prospective graduate students and postdocs:

The work in my lab in Irvine is entirely computational. The empirical components of my influenza research are done by my collaborators at the Centers for Disease Control and Prevention in Atlanta.

Prospective graduate students/postdocs should have a background or strong interest in the evolution of infectious disease, molecular evolution, computational biology and statistics.

Postdocs must have at least basic computer programming skills.

Note to undergrads and high school students:

Because my research is computational it is probably not appropriate for most undergraduates seeking 199 research experience in infectious disease. I would be happy to help direct undergraduates to laboratories where they might gain wet-lab experience.

I do not use high school volunteers in my research.

 

I study the evolution of infectious disease using the techniques of molecular phylogenetics, population genetics and protein homology modeling. In particular, I develop and apply computational techniques to study how antigenic proteins on the surfaces of pathogens evolve in response to host immune defenses.

Most of my efforts constitute basic research: I develop and test hypotheses about evolutionary processes. However, I also collaborate with scientists at public health agencies such as the CDC in applying my results to current efforts in disease surveillance, predictindexion and vaccine development.

My research primarily focuses on the influenza virus, which with subsequent pneumonia is the sixth leading cause of death in the US. I also work on the bacteria Chlamydia, which is the major cause of preventable human blindness and also the leading cause of venereal disease worldwide.

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Influenza


Fitch, W.M., R.M. Bush, C.A. Bender and N.J. Cox. 1997. Long term trends in the evolution of H(3) HA1 human influenza type A. Proceedings of the National Academy of Sciences 94: 7712-7718.

Bush, R.M., W.M. Fitch, C.A. Bender and N.J. Cox. 1999. Positive selection on the H3 hemagglutinin gene of human influenza virus A. Molecular Biology and Evolution 16:1457-1465.

Bush, R. M., C.A. Bender, K. Subbaro, N.J. Cox and W.M. Fitch. 1999. Predicting the evolution of influenza A. Science 286:1921-1925.

Bush, R.M., C.B. Smith, N.J. Cox and W.M. Fitch. 2000. Effects of passage history and sampling bias on phylogenetic reconstruction of human influenza A evolution. Proceedings of the National Academy of Sciences U.S.A. 97: 6974-6980.

Bush, R.M., W.M. Fitch, C.B. Smith and N.J. Cox. 2001. Predicting influenza evolution: the impact of terminal and egg-adapted mutations. pp. 147-153 In: Options for the Control of Influenza IV. A.D.M.E. Osterhaus, N. Cox and A.W. Hampson (eds.) Elsevier Science BV, Amsterdam.

Ferguson, N.M., A.P. Galvani and R.M. Bush. 2003. Ecological and immunological determinants of influenza evolution. Nature 422:428-433.

Bush. R.M. 2004. Influenza as a model system for studying the cross-species transfer and evolution of the SARS coronavirus. Philos Trans R Soc Lond B Biol Sci. 359:1067-1073.

Bush, R.M. 2007. Influenza Evolution. pp. 199-214 in: Encyclopedic Guide to Infectious Disease Research: Modern Methodologies  M. Tibayrenc (ed.).  John Wiley and Sons. Hoboken, NJ.

Frank, S. A. and Bush, R.M. 2007. Barriers to antigenic escape by pathogens: trade-off between reproductive rate and antigenic mutability. BMC Evolutionary Biology 7:229

Huang, S.S. et al., 2010. Quantifying Interhospital Patient Sharing as a Mechanism for Infectious Disease Spread. Infection Control and Hospital Epidemiology 31(11)

Bush. R.M. 2010. Influenza Forensics. pp 109-135 in: Microbial Forensics. 2nd Edition. Budowle, B. et al., (eds). Elsevier (no pdf available due to copyright).

Amaro, R.E., R.V. Swift, L. Votapka, W.W. Li, R.C. Walker & R. M. Bush. 2011. Mechanism of 150-cavity formation in influenza neuraminidase. Nature Communications 2:388

Chlamydia

Everett, K.D.E., R.M. Bush and A.A. Andersen. 1999. Emended description of the order Chlamydiales, proposal of two new families and species, revised taxonomy of the family Chlamydiaceae including a new genus and five new species, and standard for the identification of organisms. International Journal of Systematic Bacteriology 49: 415-440.

Everett, K.D.E., S. Kahane, R.M. Bush and M.G. Friedman. 1999. An unspliced group I intron in 23S rRNA links Chlamyidales, chloroplasts and mitochondria. J. Bacteriology 181:4734-4740.

Bush, R.M. and K.D.E. Everett. 2001 Molecular evolution of the Chlamyidaceae. International Journal of Systematic Evolution and Microbiology 51:203-220.

Rodríguez-Marañón, M.J., Bush, R.M. Peterson, E.M. Schirmer, T. and L. de la Maza. 2002. Prediction of the membrane-spanning beta-strands of the major outer membrane protein of Chlamydia. Protein Science 11:1854-1861.

Reviews

Bush, R.M. Predicting adaptive evolution. 2001. Nature Reviews Genetics 2:387-392.

Bush, R.M. 2002. Influenza. pp. 576-579 in: Oxford Encyclopedia of Evolution. M. Pagel (ed.). Oxford University Press, UK. 

Bush, R.M. and N.J. Cox 2004. Influenza Evolution. pp. 175-197 in: Infectious Disease and Host-Pathogen Evolution. K.R. Dronamraju (ed.). Cambridge University Press, UK.

Pine trees & mice