U.S. Department of Energy

Pacific Northwest National Laboratory

Sean Colby

Professional Title: 
Scientist
Phone Number: 
(509) 371-6912
Email: 
sean.colby@pnnl.gov
Biography: 

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.

Education: 

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

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

Research Interests: 

Cheminformatics
Bioinformatics
Modeling and simulation
Machine learning
Deep learning
Computer vision
 

Publications: 

2018

  • Nobela O, Renslow RS, Thomas DG, Colby SM, Sitha S, Njobeh PB, du Preez L, Tugizimana F, Madala NE. Efficient discrimination of natural stereoisomers of chicoric acid, an HIV-1 integrase inhibitor. Journal of Photochemistry and Photobiology B: Biology. 2018 Dec 1;189:258-66.
  • Yesiltepe Y, Nuñez JR, Colby SM, Thomas DG, Borkum MI, Reardon PN, Washton NM, Metz TO, Teeguarden JG, Govind N, Renslow RS. An automated framework for NMR chemical shift calculations of small organic molecules. Journal of cheminformatics. 2018 Dec;10(1):52.
  • Colby SM, McClure RS, Overall CC, Renslow RS, McDermott JE. Improving network inference algorithms using resampling methods. BMC bioinformatics. 2018 Dec;19(1):376.
  • Abassi MA, Liu X, Moerto J, Moon K, Darquenne C, Kuprat A, Colby S, Garibaldi B. Toward a Smart Stethoscope: Correlation between trachea internal airway geometry and the auscultation signal response. Bulletin of the American Physical Society. 2018 Nov 19.
  • Nuñez JR, Colby SM, Thomas DG, Tfaily MM, Tolic N, Ulrich EM, Sobus JR, Metz TO, Teeguarden JG, Renslow RS. Advancing Standards-Free Methods for the Identification of Small Molecules in Complex Samples. arXiv preprint arXiv:1810.07367. 2018 Oct 17.
  • Garcellano RC, Moinuddin SG, Young RP, Zhou M, Bowden ME, Renslow RS, Yesiltepe Y, Thomas DG, Colby SM, Chouinard CD, Nagy G. Isolation of tryptanthrin and reassessment of evidence for its isobaric isostere wrightiadione in plants of the Wrightia Genus. Journal of natural products. 2018 Oct 8.
  • Colby SM, Thomas DG, Nunez JR, Baxter DJ, Glaesemann KR, Brown JM, Pirrung MA, Govind N, Teeguarden JG, Metz TO, Renslow RS. ISiCLE: A molecular collision cross section calculation pipeline for establishing large in silico reference libraries for compound identification. arXiv preprint arXiv:1809.08378. 2018 Sep 22.
  •  

2017

  • 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

2016

  • 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

2013

  • 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

2012

  • 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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