Data Scientist, Biological Sciences
Data Scientist, Biological Sciences

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.

Disciplines and Skills

  • Cheminformatics
  • Bioinformatics
  • Modeling and simulation
  • Machine learning
  • Deep learning
  • Computer vision

Education

  • BS, Bioengineering, Washington State University
  • MS, Computer Science, Georgia Institute of Technology

Publications

2019

  • Colby, S. M.; Nuñez, J. R.; Hodas, N. O.; Corley, C. D.; Renslow, R. S., Deep learning to generate in silico chemical property libraries and candidate molecules for small molecule identification in complex samples. Analytical chemistry 2019.
  • Colby, S. M.; Thomas, D. G.; Nuñez, J. R.; Baxter, D. J.; Glaesemann, K. R.; Brown, J. M.; Pirrung, M. A.; Govind, N.; Teeguarden, J. G.; Metz, T. O., ISiCLE: A quantum chemistry pipeline for establishing in silico collision cross section libraries. Analytical chemistry 2019, 91 (7), 4346-4356.
  • Nunez, J. R.; Colby, S. M.; Thomas, D. G.; Tfaily, M. M.; Toliċ, N.; Ulrich, E. M.; Sobus, J. R.; Metz, T. O.; Teeguarden, J. G.; Renslow, R. S., Evaluation of In Silico Multi‐Feature Libraries for Providing Evidence for the Presence of Small Molecules in Synthetic Blinded Samples. Journal of Chemical Information and Modeling 2019.
  • Rod, K. A.; Um, W.; Colby, S. M.; Rockhold, M. L.; Strickland, C. E.; Han, S.; Kuprat, A. P., Relative permeability for water and gas through fractures in cement. PloS one 2019, 14 (1).

2018

  • Colby, S. M.; McClure, R. S.; Overall, C. C.; Renslow, R. S.; McDermott, J. E., Improving network inference algorithms using resampling methods. BMC bioinformatics 2018, 19 (1), 1-9.
  • Yesiltepe, Y.; Nuñez, J. R.; Colby, S. M.; Thomas, D. G.; Borkum, M. I.; Reardon, P. N.; Washton, N. M.; Metz, T. O.; Teeguarden, J. G.; Govind, N., An automated framework for NMR chemical shift calculations of small organic molecules. Journal of cheminformatics 2018, 10 (1), 1-16.
  • Garcellano, R. C.; Moinuddin, S. G.; Young, R. P.; Zhou, M.; Bowden, M. E.; Renslow, R. S.; Yesiltepe, Y.; Thomas, D. G.; Colby, S. M.; Chouinard, C. D., Isolation of tryptanthrin and reassessment of evidence for its isobaric isostere wrightiadione in plants of the Wrightia Genus. Journal of natural products 2018, 82 (3), 440-448.
  • Nobela, O.; Renslow, R. S.; Thomas, D. G.; Colby, S. M.; Sitha, S.; Njobeh, P. B.; Du Preez, L.; Tugizimana, F.; Madala, N. E., Efficient discrimination of natural stereoisomers of chicoric acid, an HIV-1 integrase inhibitor. Journal of Photochemistry and Photobiology B: Biology 2018, 189, 258-266.

2017

  • White III, R. A.; Rivas-Ubach, A.; Borkum, M. I.; Köberl, M.; Bilbao, A.; Colby, S. M.; Hoyt, D. W.; Bingol, K.; Kim, Y.-M.; Wendler, J. P., The state of rhizospheric science in the era of multi-omics: a practical guide to omics technologies. Rhizosphere 2017, 3, 212-221.
  • White, R. A.; Borkum, M. I.; Rivas-Ubach, A.; Bilbao, A.; Wendler, J. P.; Colby, S. M.; Köberl, M.; Jansson, C., From data to knowledge: the future of multi-omics data analysis for the rhizosphere. Rhizosphere 2017, 3, 222-229.

2016

  • Colby, S. M.; Kabilan, S.; Jacob, R. E.; Kuprat, A. P.; Einstein, D. R.; Corley, R. A., Comparison of realistic and idealized breathing patterns in computational models of airflow and vapor dosimetry in the rodent upper respiratory tract. Inhalation toxicology 2016, 28 (4), 192-202.
  • Kabilan, S.; Suffield, S. R.; Recknagle, K. P.; Jacob, R. E.; Einstein, D. R.; Kuprat, A. P.; Carson, J. P.; Colby, S. M.; Saunders, J. H.; Hines, S., Computational fluid dynamics modeling of Bacillus anthracis spore deposition in rabbit and human respiratory airways. Journal of Aerosol Science 2016, 99, 64-77.

​​​​​​​2013

  • Jacob, R. E.; Colby, S. M.; Kabilan, S.; Einstein, D. R.; Carson, J. P., In situ casting and imaging of the rat airway tree for accurate 3D reconstruction. Experimental lung research 2013, 39 (6), 249-257.

​​​​​​​2012

  • Carson, J. P.; Kuprat, A. P.; Colby, S. M.; Davis, C. A.; Basciano, C. A.; Greene, K.; Feo, J. T.; Kennedy, A. In Detecting distance between injected microspheres and target tumor via 3D reconstruction of tissue sections, 2012 Annual International Conference of the IEEE Engineering in Medicine and Biology Society, IEEE: 2012; pp 1149-1152.