U.S. Department of Energy

Pacific Northwest National Laboratory

Sean Colby

Sean Colby
Professional Title: 
Phone Number: 
(509) 371-6912

Sean Colby is an expert in the application of computational resources to solve multidisciplinary problems, often involving massive datasets (big data).  His focus has thus far included cheminformatics, bioinformatics, plant and soil sciences, and human health science, with a particular focus on deep learning as applied to these fields. He brings a fresh technical perspective to projects, applying state-of-the-art tools to address anticipated challenges.


2016  M.S., Computer Science, Georgia Institute of Technology, Atlanta, GA

2013  B.S., Bioengineering, Washington State University, Pullman, WA

Research Interests: 

Modeling and simulation
Machine learning
Deep learning
Computer vision



  • White RA, III, A Rivas-Ubach, MI Borkum, M Koberl, A Bilbao Pena, SM Colby, DW Hoyt, AK Bingol, YM Kim, JP Wendler, KK Hixson, and GC Jansson. 2017. "The state of rhizospheric science in the era of multi-omics: A practical guide to omics technologies." Rhizosphere 3(2):212-221.  doi:10.1016/j.rhisph.2017.05.003
  • White RA, III, AR Panyala, KA Glass, SM Colby, KR Glaesemann, GC Jansson, and JK Jansson. 2017. "MerCat: a versatile k-mer counter and diversity estimator for database-independent property analysis obtained from metagenomic and/or metatranscriptomic sequencing data." PeerJ Preprints 5:Article No. e2825v1. doi:10.7287/peerj.preprints.2825v1
  • White RA, III, JM Brown, SM Colby, CC Overall, JY Lee, JD Zucker, KR Glaesemann, GC Jansson, and JK Jansson. 2017. "ATLAS (Automatic Tool for Local Assembly Structures) - A Comprehensive Infrastructure for Assembly, Annotation, and Genomic Binning of Metagenomic and Metaranscripomic Data." PeerJ Preprints 5:,doi:10.7287/peerj.preprints.2843v1
  • White RA, III, MI Borkum, A Rivas-Ubach, A Bilbao Pena, JP Wendler, SM Colby, M Koberl, and GC Jansson. 2017. "From data to knowledge: The future of multi-omics data analysis for the rhizosphere." Rhizosphere 3(2):222-229.  doi:10.1016/j.rhisph.2017.05.001


  • Colby SM, S Kabilan, RE Jacob, AP Kuprat, DR Einstein, and RA Corley. 2016. "Comparison of realistic and idealized breathing patterns in computational models of airflow and vapor dosimetry in the rodent upper respiratory tract." Inhalation Toxicology 28(4):192-202. doi:10.3109/08958378.2016.1150367
  • Kabilan S, SR Suffield, KP Recknagle, RE Jacob, DR Einstein, AP Kuprat, JP Carson, SM Colby, JH Saunders, S Hines, JG Teeguarden, TM Straub, M Moe, S Taft, and RA Corley. 2016. "Computational fluid dynamics modeling of Bacillus anthracis spore deposition in rabbit and human respiratory airways." Journal of Aerosol Science 99:64-77. doi:10.1016/j.jaerosci.2016.01.011
  • Kabilan S, SR Suffield, KP Recknagle, RE Jacob, DR Einstein, AP Kuprat, JP Carson, SM Colby, JH Saunders, S Hines, JG Teeguarden, TM Straub, M Moe, S Taft, and RA Corley. 2016. "Computational Fluid Dynamics Modeling of Bacillus anthracis Spore Deposition in Rabbit and Human Respiratory Airways." Journal of Aerosol Science 99:64-77. doi:10.1016/j.jaerosci.2016.01.011


  • Jacob RE, SM Colby, S Kabilan, DR Einstein, and JP Carson. 2013. "In Situ Casting and Imaging of the Rat Airway Tree for Accurate 3D Reconstruction." Experimental Lung Research 39(6):249-257.  doi:10.3109/01902148.2013.801535


  • Carson JP, AP Kuprat, SM Colby, CA Davis, C Basciano, K Greene, JT Feo, and A Kennedy. 2012. "Detecting Distance between Injected Microspheres and Target Tumor via 3D Reconstruction of Tissue Sections." In 2012 Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC), August 28 - September 1, San Diego, California, pp. 1149-1152.  IEEE, Piscataway, NJ.  doi:10.1109/EMBC.2012.6346139
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