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Staff information


Pubudu Handakumbura

Environ Transform & Interact
Pacific Northwest National Laboratory
PO Box 999
MSIN: K8-93
Richland, WA 99352


Dr. Pubudu Handakumbura is a Staff Scientist and a Team Lead in the Environmental Transformations and Interactions group at EMSL. She is using systems and synthetic biology approaches to study plant-microbe-soil interactions. The main focus areas of her current research are to develop biomarkers to engineer and improve crop resilience under changing climates, to improve photosynthetic performance and carbon partition in plants and enhancing feed stock attributes in lignocellulosic biomass for bioenergy production. Dr. Handakumbura has extensive experience in advanced molecular biology techniques and genetic engineering, plant tissue culture and plant multi-omics techniques. She leads the Molecular Plant Phenotyping efforts at EMSL.

Research Interests

  • Multi-omics approaches in Molecular Plant Phenotyping
  • Lignocellulosic feedstock engineering
  • Plant-microbe-soil interactions

Education and Credentials

  • 2014, Ph.D., Plant Biology, University of Massachusetts Amherst, MA
  • 2007, B.Sc., Plant Biotechnology, University of Colombo, Sri Lanka

Affiliations and Professional Service

  • Member of the American Association for the Advancement of Science (AAAS)
  • Member of the American Society for Plant Biologists (ASPB)

Awards and Recognitions

  • 2015, Best poster presentation in postdoctoral category at Northeast regional American Society of Plant Biologists conference
  • 2012-2013, Gilgut Fellowship, University of Massachusetts Amherst, MA
  • 2012 & 2013, American Society of Plant Biologists national travel awards
  • 2012, Best oral presentation, Life Sciences Graduate Research Symposium, University of Massachusetts Amherst, MA
  • 2007, Professor BLT de Silva memorial prize for Botany, University of Colombo
  • 2007, Sir Nigel Ball Award for Botany, University of Colombo
  • 2007, Gold medalist for outstanding Science Student of the year, University of Colombo

PNNL Publications


  • Abraham-Juarez M.J., A. Schrager-Lavelle, J. Man, C. Whipple, P. Handakumbura, C. Babbitt, and M. Bartlett. 2020. "Evolutionary Variation in MADS Box Dimerization Affects Floral Development and Protein Abundance in Maize." The Plant Cell 32, no. 11:3408-3424. PNNL-SA-155208. doi:10.1105/tpc.20.00300
  • Liu W., L. Huang, R.E. Komorek, P. Handakumbura, Y. Zhou, D. Hu, and M.H. Engelhard, et al. 2020. "Correlative Surface Imaging Reveals Chemical Signatures for Bacterial Hotspots on Plant Roots." Analyst 145, no. 2:393-401. PNNL-SA-149225. doi:10.1039/C9AN01954E


  • Handakumbura P., B.A. Stanfill, A. Rivas-Ubach, D.C. Fortin, J.P. Vogel, and G.C. Jansson. 2019. "Metabotyping as a Stopover in Genome-to-Phenome Mapping." Scientific Reports 9, no. 1:Article Number 1858. PNNL-SA-135368. doi:10.1038/s41598-019-38483-0


  • Ahkami A., R.A. White, P. Handakumbura, and G.C. Jansson. 2017. "Rhizosphere Engineering: Enhancing Sustainable Plant Ecosystem Productivity in a Challenging Climate." Rhizosphere 3, no. 2:233-243. PNNL-SA-124740. doi:10.1016/j.rhisph.2017.04.012
  • Handakumbura P., K.K. Hixson, S.O. Purvine, G.C. Jansson, and L. Pasa Tolic. 2017. "Plant iTRAQ-based proteomics." Current Protocols in Plant Biology 2, no. 2:158-172. PNNL-SA-123355. doi:10.1002/cppb.20052

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