John Parkinson, PhD


To survive and persist within their human hosts, infectious disease agents such as bacterial pathogens and parasites have acquired a vast battery of molecular innovations. With the recent availability of genomics and proteomics resources, members of our lab use computational approaches to identify the molecules and pathways that enable these organisms to infect their hosts. Capitalizing on recent developments in the analysis of complex microbial communities, we are also investigating how the composition and function of a patients microbiome can modify the ability of pathogens and parasites to cause disease. Ultimately our aim is to identify processes, encoded by the parasite, the host, or even the host microbiome, that can be targeted for therapeutic intervention.

Selected publications:

  1. Babu M.*#, Bundalovic-Torma C.*, Calmettes C.,* Phanse S., Zhang Q., Jiang Y., Minic Z., Kim S., Mehla J., Gagarinova A., Rodionova I., Kumar A., Guo H., Kagan O., Pogoutse O., Aoki H., Deineko V., Caufield J. H., Holtzapple E., Zhang Z., Vastermark A., Pandya Y., Lai C.C., El Bakkouri M., Hooda Y., Shah M., Burnside D., Hooshyar M., Vlasblom J., Rajagopala S.V., Golshani A., Wuchty S., Greenblatt J.F., Saier M.,# Uetz P.,# Moraes T.F.,# Parkinson J.# and Emili A.# (2018) Global landscape of cell envelope protein complexes in Escherichia coli. Nature Biotechnology. 36: 103-112
  2. Xiong X., Bales C.E., Ir D., Robertson C.E., McManaman J.L., Frank D.N.# and Parkinson J.# (2017) Perilipin-2 modulates dietary fat-induced microbial global gene expression profiles in the mouse intestine. Microbiome. 5:117.
  3. Cotton J.A., Bennuru S., Grote A., Harsha B., Tracey A., Beech R., Doyle S.R., Dunn M., Hotopp J.C.D., Holroyd N., Kikuchi T., Lambert O., Mhashilkar A., Mutowo P., Nursimulu N., Ribeiro J.M.C., Rogers M.B., Stanley E., Swapna L.S., Tsai I.J., Unnasch T.R., Voronin D., Parkinson J., Nutman T.B., Ghedin E., Berriman M. and Lustigman S. (2016) The genome of Onchocerca volvulus, agent of river blindness. Nature Microbiology. 2:16216
  4. Blazejewski T., Nursimulu N., Pszenny V., Dangoudoubiyam S., Namasivayam S., Chiasson M.A., Chessman K., Tonkin M., Swapna L.S., Hung S.S., Bridgers J., Ricklefs S.M., Boulanger M.J., Dubey J.P., Porcella S.F., Kissinger J.C., Howe D.K., Grigg M.E. and Parkinson J. (2015) Systems based analysis of the Sarcocystis neurona genome identified pathways that contribute to a heteroxenous life cycle. mBio. 6(1). pii: e02445-14.
  5. Song, C., Chiasson, M.A., Nursimulu, N., Hung, S.S., Wasmuth, J., Grigg, M.E., and Parkinson, J. (2013) Metabolic reconstruction identifies strain-specific regulation of virulence in Toxoplasma gondii. Molecular Systems Biology. 9: 708.