Minseung Kim UC Davis Genome Center 5302 GBSF [email protected] (530)746-1574

Education Ph.D. in 2013 - Present University of California at Davis, Davis, CA Dissertation: Big data on small organisms: Data integration and genome-scale multi-omics predictive modeling for microbial species Advisor: Dr. Ilias Tagkopoulos M.S. in Computer Science Feb 2010 Columbia University, New York, NY B.S. in Computer Science Aug 2008 Illinois Institute of Technology, Chicago, IL Summa Cum Laude, double minors in Applied and Linguistics B.S. in Computer Engineering Aug 2008 Hongik University, Seoul, Republic of Korea Research & Work Experience Intern, PIPA LLC, 2016 - present Intern, working with corporate clients to provide custom ML/AI solutions as a team lead. Graduate Student Researcher, Genome Center, University of California at Davis 2013 - present Machine learning and deep learning analytics for multi-omics data integration. Advisor: Ilias Tagkopoulos Research Associate, Institute of Life Science and Biotechnology, Yonsei University, S. Korea 2011 - 2013 Visiting Scholar, Department of Chemistry, University of California at Berkeley 2012 Prediction of cancer susceptibility using machine learning methods. Advisor: Dr. Sung-Hou Kim Researcher, Samsung Biomedical Research Institute, Samsung Electronics Co., Ltd., S. Korea 2010 - 2011 Bioinformatic analysis for Korean cancers. Advisor: Dr. Joobae Park & Dr. Duk-Hwan Kim Graduate Research Assistant & Independent Study, Columbia University 2008 - 2009 Computational Genomics Lab, Advisor: Dr. Itsik Pe’er Undergraduate Research Assistant, Illinois Institute of Technology 2007 Natural Language Processing Lab, Advisor: Dr. Shlomo Argamon Undergraduate Research Intern, Korea Advanced Institute of Science and Technology Summer 2006 Artificial Intelligence and Media Lab, Advisor: Dr. Hyun Seung Yang Journal Publications and Preprints [12] KJ Kim, N. Rai, M. Kim, I. Tagkopoulos. “A network-based model for drug repurposing in Rheumatoid Arthritis” PLoS Computational. Biology. under review (2018) [11] N. Rai, L. Huynh, M. Kim, I. Tagkopoulos. “Genome-wide genetic and transcriptional responses of Escherichia coli during long-term chemostat experimentation” mBio under review (2018) [10] X. Wang, V. Zorraquino, M. Kim, et al. “Data-driven prediction of E. coli evolution at a gene level” Nature Communications accepted (2018) [09] KJ Kim, M. Kim, I Tagkopoulos. “Compendium of Synovial Signatures Identifies Pathologic Characteristics for Predicting Treatment Response in Rheumatoid Arthritis”, bioRxiv, 2018 [08] M. Kim, and I. Tagkopoulos. “Data integration and predictive modeling methods for multi-omics datasets. Molecular Omics (2018). [07] M. Kim, A. Eetemadi, and I. Tagkopoulos. “DeepPep: Deep proteome inference from peptide profiles. PLoS Computational. Biology. 13.9 (2017): e1005661. [06] M. Kim, N. Rai, V. Zorraquino, and I. Tagkopoulos, “Multi-omics integration accurately predicts cellular state in unexplored conditions for Escherichia coli”, Nature Communications 7:13090 (2016) doi: 10.1038/ncomms13090

1 [05] V. Zorraquino, M. Kim, et al. The genetic and transcriptional basis of short and long term adaptation across multiple stresses in Escherichia coli. Molecular Biology and Evolution (2016): msw269 [04] M. Kim, V. Zorraquino, and I. Tagkopoulos, “Microbial Forensics: Predicting phenotypic characteristics and environmental conditions from large-scale gene expression profiles”, PLoS Computational Biology, 2015; 11.3:e1004127-e1004127 [03] M. Kim and SH Kim, “Empirical prediction of genomic susceptibilities for multiple cancer classes.”, Proceedings of the National Academy of Sciences 2014; 111(5):1921-1926 [02] DH Kim, SE Park, M. Kim et al. “A functional single nucleotide polymorphism at the promoter region of Cyclin A2 is associated with increased risk of colon, liver, and lung cancers”, Cancer, 2011; 117(17):4080-91 [01] EE Kenny, M. Kim, A Gusev et al. “Increased power of mixed models facilitates association mapping of 10 loci for metabolic traits in an isolated population” Human Molecular Genetics 2011; 20(4):827-39 Conference Publications and Presentations [13] “Multi-omics integration accurately predicts cellular state in unexplored conditions”, PEGS, 2018; (invited talk) [12] “DeepPep: deep proteome inference from peptide profiling”, Blue Waters Symposium, 2016; (oral) [11] “Multi-omics integration accurately predicts cellular state in unexplored conditions”, UCD IGPS, 2016; (oral) [10] “Multi-omics integration accurately predicts cellular state in unexplored conditions”, RECOMB, Santa Monica, CA, April 2016; (poster) [09] “Multi-omics integration and optimal experimental design accurately predicts cellular and growth dynamics”, Q-Bio, Honolulu, HI, 2016; (oral) [08] “Multi-omics integration and optimal experimental design accurately predicts cellular and growth dynamics”, ISCB/RECOMB RGS, Philadelphia, PA, 2015; (oral and poster) [07] L. Huynh, M. Kim and I. Tagkopoulos, “Integration of Circuit Design Automation and Genome-scale Modeling”, IWBDA, Boston, MA, 2014 [06] “Graph-based integrated learning framework for whole-cell modeling”, NetSci, Berkeley, CA, 2014; (poster) [05] “M. Kim, et al., ”An integrative genome-scale E. coli model and targeted experimentation methodology for systems and synthetic biology”, Q-Bio, Hawaii, 2014 [04] “Efficient genotype imputation for merged platforms”, Inje University, Busan, South Korea, 2010; (invited talk) [03] “Method comparison for analyzing association studies in a founder population”, C2B2/MagNet, New York, NY, 2009; (poster) [02] “Opinion mining of news corpus”, CAURS, Chicago, IL, 2007 ; (poster) [01] M. Kim, TM Kim, HS Yang, “Optimal trajectory generation of compass gait biped based on passive dynamic walking”, IASTED AIA, 2007; (oral and proceedings) Awards & Honors Graduate Student Research Fellowship, University of California at Davis 2013 - present Travel Award, {RECOMB, UCD} 2015-2016 Graduate Student Researcher Award, University of California at Davis Summer {2014,2015,2017} Undergraduate Student Researcher Award, Illinois Institute of Technology Summer 2007 International Exchange Student Scholarship, Hongik University 2006 - 2008 Chang-Jo Scholarship, Hongik University Fall 2005 Patents [1] Computer Implemented Methods for Analyzing Genomic or Epigenomic Variations (PCT international patent application) Professional Experience Journal Reviewer BMC BioData Mining Teaching Experience Teaching Assistant, {Machine Learning, , Discrete Mathematics}, UCD 2014-2015

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