Data Scientist
Data Scientist

Biography

Allison Thompson is a data scientist with the Systems Modeling and Computational Science team in PNNL’s Environmental Molecular Sciences Division and the Environmental Molecular Sciences Laboratory (EMSL) user program. As an expert in statistical analysis and visualization of biological "big data" she has helped develop numerous R packages for efficient, reproducible, and accurate analyses of omics data, including proteomics, metabolomics, and genomics. Her research at PNNL includes statistical and visual integration of multiple data types; the application of high performance computing and statistical techniques to handle the amount of data being generated by current -omics technologies; and soil organic matter, from multiple standpoints. Thompson has a strong background in communicating with subject matter experts in statistics, biology, chemistry, and computer science, and determining ways to integrate domain knowledge from these fields. ​​​

 

Research Interest

  • Data analysis and visualization 

  • Data integration 

  • Omics 

  • Plant-soil-microbe interactions 

  • Nutrient cycling in soils 

Education

  • MS in Bioinformatics and Computational Biology, University of Idaho, 2014 

  • BS in Biological and Agricultural Engineering, University of Idaho, 2011 

Awards and Recognitions

  • Mentor of the Year, Earth and Biological Sciences Directorate BESTies, PNNL (2019) 

Publications

2020 

  • Kasanke, C. P., Q. Zhao, S. L. Bell, A. M. Thompson, and K. S. Hofmockel. 2020. “Can switchgrass increase carbon accrual in marginal soils? The importance of site selection.” Global Change Biology Bioenergy. https://doi.org/10.1111/gcbb.12777 

  • Bhattacharjee, A., A. M. Thompson, K. C. Schwarz, M. C. Burnet, Y. M. Kim, J. R. Nunez, S. J. Fansler, Y. Farris, C. J. Brislawn, T. O. Metz, R. S. McClure, R. S. Renslow, L. Shor, J. K. Jansson, K. S. Hofmockel, and C. R. Anderton. 2020. “Soil Microbial EPS Resiliency Is Influenced by Carbon Source Accessibility.” Soil Biology and Biochemistry 151. https://doi.org/10.1016/j.soilbio.2020.108037. 

  • Bramer L.M., A.M. White, K.G. Stratton, A.M. Thompson, D.M. Claborne, K.S. Hofmockel, and L. McCue. 2020. "ftmsRanalysis: An R package for exploratory data analysis and interactive visualization of FT-MS data." PLoS Computational Biology 16, no. 3:Article No. e1007654. PNNL-SA-152118. doi:10.1371/journal.pcbi.1007654 

  • Zhao Q., S.J. Callister, A.M. Thompson, R.K. Kukkadapu, M. Tfaily, L.M. Bramer, and N. Qafoku, et al. 2020. "Strong mineralogic control of soil organic matter composition in response to nutrient addition across diverse grassland sites." Science of Total Environment 736. PNNL-SA-144529. doi:10.1016/j.scitotenv.2020.137839 

2019 

  • Stratton K.G., B.M. Webb-Robertson, L. McCue, B.A. Stanfill, D.M. Claborne, I.G. Godinez, and T. Johansen, et al. 2019. "pmartR: Quality Control and Statistics for Mass Spectrometry-Based Biological Data." Journal of Proteome Research 18, no. 3:1418-1425. PNNL-SA-123105. doi:10.1021/acs.jproteome.8b00760 

2018 

  • Stanfill B.A., E.S. Nakayasu, L.M. Bramer, A.M. Thompson, C.K. Ansong, T. Clauss, and M.A. Gritsenko, et al. 2018. "Quality Control Analysis in Real-time (QC-ART): A Tool for Real-time Quality Control Assessment of Mass Spectrometry-based Proteomics Data." Molecular and Cellular Proteomics 17, no. 9:1824-1836. PNNL-SA-129934. doi:10.1074/mcp.RA118.000648