PNNL

Joon-Yong Lee has worked as a scientist at PNNL since 2017. After he earned his PhD in electrical engineering at the Korea Advanced Institute of Science and Technology in 2011, he worked at Advanced Telecommunications Research International.

• Multi-omics data analysis
• Omics data visualization
• Machine learning
• Evolutionary computation
• Community-based metabolic modeling
• Metabolic network inference

• PhD in Electrical Engineering, Korea Advanced Institute of Science and Technology, 2011
• MS in Electrical Engineering and Computer Science, Korea Advanced Institute of Science and Technology, 2004
• BS in Engineering, Ajou University, 2002

• Postdoctoral Research Assistant, Integrative Omics, Biological Sciences Division, PNNL (2014-2017)
• Postdoctoral Research Assistant, Department of Genetics, Development, and Cell Biology, Iowa State University (2013-2014)
• Researcher, Intelligent Robotics and Communication Laboratories, Advanced Telecommunications Research International, Japan (2011-2013)

• Best Poster Award in 5th Symposium on Biological Data Visualization, BioVis 2015 at Intelligent Systems for Microbiology/European Conference on Computational Biology, 2015

2020

• Lee J., N.C. Sadler, R.G. Egbert, C.R. Anderton, K.S. Hofmockel, J.K. Jansson, and H. Song. 2020. "Deep Learning Predicts Microbial Interactions from Self-organized Spatiotemporal Patterns." Computational and Structural Biotechnology Journal 18. PNNL-SA-150281. doi:10.1016/j.csbj.2020.05.023
• Lee J., S. Haruta, S. Kato, H. Bernstein, S.R. Lindemann, D. Lee, and J.K. Fredrickson, et al. 2020. "Prediction of Neighbor-dependent Microbial Interactions from Limited Population Data." Frontiers in Microbiology 10. PNNL-SA-144026. doi:10.3389/fmicb.2019.03049

2019

• Song H., J. Lee, S. Haruta, W.C. Nelson, D. Lee, S.R. Lindemann, and J.K. Fredrickson, et al. 2019. "Minimal Interspecies Interaction Adjustment (MIIA): Inference of Neighbor-Dependent Interactions in Microbial Communities." Frontiers in Microbiology 10. PNNL-SA-131990. doi:10.3389/fmicb.2019.01264

2018

• Lee J., G.M. Fujimoto, R.E. Wilson, H. Wiley, and S.H. Payne. 2018. "Blazing Signature Filter: a library for fast pairwise similarity comparisons." BMC Bioinformatics 19. PNNL-SA-126956. doi:10.1186/s12859-018-2210-6
• Lee J., H. Choi, C. Colangelo, D. Davis, M. Hoopmann, L. Kall, and H. Lam, et al. 2018. "ABRF Proteome Informatics Research Group (iPRG) 2016 Study: Inferring Proteoforms from Bottom-up Proteomics Data." Journal of Biomolecular Techniques:JBT 29, no. 2:39-45. PNNL-SA-133941. doi:10.7171/jbt.18-2902-003
• Song H., W.C. Nelson, J. Lee, R.C. Taylor, C.S. Henry, A.S. Beliaev, and D. Ramkrishna, et al. 2018. "Metabolic Network Modeling for Computer-Aided Design of Microbial Interactions." In Emerging Areas in Bioengineering, edited by HN Chang, et al. 793-801. Weinheim:Wiley-VCH Verlag GmbH & Co. PNNL-SA-115176.  doi:10.1002/9783527803293.ch45

2017

• Dasgupta A., J. Lee, R.E. Wilson, R.A. Lafrance, N.O. Cramer, K.A. Cook, and S.H. Payne. 2017. "Familiarity Vs Trust: A Comparative Study of Domain Scientists’ Trust in Visual Analytics and Conventional Analysis Methods." IEEE Transactions on Visualization and Computer Graphics 23, no. 1:271-280. PNNL-SA-117411. doi:10.1109/TVCG.2016.2598544
• White R.A., J.M. Brown, S.M. Colby, C.C. Overall, J. Lee, J.D. Zucker, and K.R. Glaesemann, et al. 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. PNNL-SA-124317. doi:10.7287/peerj.preprints.2843v1

2016

• Henry C.S., H.C. Bernstein, P. Weisenhorn, R.C. Taylor, J. Lee, J.D. Zucker, and H. Song. 2016. "Microbial Community Metabolic Modeling: A Community Data-Driven Network Reconstruction." Journal of Cellular Physiology 231, no. 11:2339-2345. PNNL-SA-118336. doi:10.1002/jcp.25428