Role: Faculty
Title: Assistant Professor
Office No: Rm 129
Address: 485 E. Gray St
Phone: (502)852-3525
Fax: (502)852-3294
E-mail: s0kim023 at louisville dot edu

- Assistant Professor (2009-current), Department of Bioinformatics and Biostatistics, University of Louisville, Louisville, KY, USA.
- Adjunct Assistant Professor (2009-current), Indiana University School of Medicine, Indianapolis, IN, USA.
- Research Associate in Biostatistics. 2009. Indiana University School of Medicine, Indianapolis, IN, USA.
- Postdoctoral Research Fellow in Biostatistics. 2008. Indiana University School of Medicine, Indianapolis, IN, USA.
- Postdoctoral Research Fellow in Comparative Genomics. 2006. Georgia Institute of Technology, Atlanta, GA, USA.
- Visiting Student in Information Sciences. 2004. University of Pittsburgh, Pittsburgh, PA, USA.
- Ph.D. in Applied Statistics (Graphical Models: Prof. Sung-Ho Kim). 2005. KAIST, Daejeon, Korea.
- M.S. in Applied Mathematics (Approximation Theory: Prof. Kil Hyun Kwon). 2000. KAIST, Daejeon, Korea.
- M.S. course in Mathematics (Several Complex Analysis). 1998. Chonnam National University, Gwangju, Korea.
- B.S. in Mathematics. 1996. Chonnam National University, Gwangju, Korea.
- Teaching Certificate in Mathematics Education. 1996. Chonnam National University, Gwangju, Korea.

I am an applied statistician, focusing on missing data analysis, time-series (longitudinal) data analysis, diagnosis, machine learning, and computational/systems biology, particularly using graphical models, ordinary differential kinetic model, EM-type and MCMC algorithms. My research interests lie in the development of novel statistical methods and models for biological and clinical data, and I have participated in various research projects, including speech pattern recognitions, decision support systems, comparative genomics/bioinformatics, and pharmacokinetics. Currently, I am developing statistical methodologies on three topics: Metabolomics, Pharmacokinetics, Cancer Screening, and Graphical Models.

-Metabolomics (collaborating with Dr. Xiang Zhang, Department of Chemistry): Peak Detection; Peak Alignment; Peak Identification; Peak Normalization; Network Construction; Biomarker Discovery
-Pharmacokinetics/Pharmacodynamics/Pharmacogenomics (collaborating with Dr. Lang Li, Indiana University School of Medicine): Whole Body-based (physiologically based) Pharmacokinetic analysis (WBPBPK); Global Optimization and Statistical Identifiability for Nonlinear Mixed-Effect Models
-Cancer Screeing
-Graphical Models: Hyper-EM for Large Continuous Data; GM-based Optimization Algorithms

- PHST691: Bayesian Inference (Spring 2011)
- PHBI750: Statistical Methods for Bioinformatics (Fall 2010; Fall 2009)
- PHBI751: High through-put data analysis (with Dr. Datta; Spring 2010)
- PHST602: Biostatistics Seminar Series (Spring 2010)

- Indiana University Nominee for Burroughs Wellcome Fund: 2009 Career Awards at the Scientific interface
- Presidential Trainee Award. 2008. American Society for Clinical Pharmacology and Therapeutics (ASCPT), Alexandria, VA
- Abroad Collaborative Research. 2004. Korea Science and Engineering Foundation (KOSEF), Daejeon, Korea

-Zhang, J.; Fang, A.; Wang, B.; Bogdanov, B.; Kim, S. H.; Zhou, Z.; McClain, C.; Zhang, X. iMatch, A retetion index tool for analysis of gas chromatography-mass spectrometry data. J. Chromatogr. A. In press.
-1.Wang, B.; Fang, A.; Shi, X.; Kim, S.; Zhang, X. A comprehensive peak alignment algorithm for two-dimensional gas chromatography time-of-flight mass spectrometry. 2011 International Conference on Intelligent Computing (ICIC’11), Aug 11-14, Zhengzhou, Henan, China.
-I Koo, X Zhang, and S Kim. 2011. “Wavelet and Fourier transforms-based similarity approaches for compound identification on GC data,” Analytical Chemistry, in press
- S Kim, I Koo, A Fang, and X Zhang. 2011. “Simith-Waterman peak alignment for two-dimensional gas chromatography mass spectrometry,” BMC Bioinformatics, 12:235.
- S Kim, A Fang, B Wang, J Jeong, and X Zhang. 2011. “An optimal peak alignment for comprehensive two-dimensional gas chromatography mass spectrometry using mixture similarity measure,” Bioinformatics, 27, 1660-1666
- Zhao, Y.; Zhang, J.; Wang, B.; Kim, S.; Fang, A.; Bogdanov, B.; Zhang, X. 2011. “A method of calculating the second dimensional retention index in comprehensive two-dimensional gas chromatography time-of-flight mass spectrometry,” Journal of Chromatography A. 1218, 2577-2583.
- I Koo, X Zhang, and S Kim. 2011. “Comparison of spectral similarity measures for compound identification,” Bioinformatics and Biomedical Engineering (iCBBE), 2011 5th International Conference, May 10-12, Wuhan, China.
- Y-T Chen, J Zhang, X Zhang, and S Kim. 2011. “Statistical analysis of gas chromatography retention index database,” Bioinformatics and Biomedical Engineering (iCBBE), 2011 5th International Conference, May 10-12, Wuhan, China.

-S.Kim and L.Li. 2011. ``A Switching Markov Chain Monte Carlo Method for Statistical Identifiability of Nonlinear Pharmacokinetics Models," Statistica Sinica, in press
-S.Kim and L.Li. 2011. “An Efficient Global Search and Numerical Ideintifiablity Algorithm on Non-liner Mixed-Effect Models,” Journal of Pharmacokinetics and Pharmacodynamics, in press
- S.Kim, L.Li. 2011. “Bayesian Monte Carlo Markov Chain (MCMC) two-stage approaches on non-linear mixed-effect pharmacokinetic models,” Clinical Pharmacology and Therapeutics 89, p. S66, OIII-A-3
- Vuppalanchi R, Juluri R, Kim S, Thong N, Gorski, C, Chalasani N, Hall S. 2010. “Drug Induced QT Prolongation in Cirrhotic Patients with Transjugular Intrahepatic Portosystemic Shunt,” Journal of Clinical Gastroenterology, in press
- Wang Z, Kim S, Quinney S, and Li L. 2010. “Non-compartment-model to Two Compartment-model Transformation analysis of Midazolam Pharmacokinetics Data,” BMC Systems Biology, 4, pp. 1-8.
- S. Kim, L. Li. 2010. “A global search and numerical identifiability algorithm," Clinical Pharmacology and Therapeutics 87, p. S64, PII-79
- Mias J, Jin Y, Marunde RL, Kim S, Quinney S, Radovich M, Li L, Hall SD. 2009. “Association of genotypes of the CYP3A cluster with midazolam disposition in vivo,” Pharmacogenomics Journal, in press.
- Re JM, Sikora MJ, Henry NL, Li L, Kim S, Oesterreich S, Skaar T, Nguyen A, Desta Z, Storniolo AM, Flockhart DA, Hayes DF, and Stearns V. 2009. “Cytochrome P450 2D6 Activity Predicts Adherence to Tamoxifen Therapy," Pharmacogenomics Journal, 9(4), pp. 258-264.
- J Zhou, Zi Qin, S Kim, Z Wang, M Yu, JY Chien, A Lucksiri, SD Hall, and L Li. 2009. “A New Probabilistic Rule for Drug-Drug Interaction Prediction," Journal of Pharmacokinetics and Pharmacodynamics, 36(1), pp. 1-18.
- Z Wang, S Kim, SK Quinney, Y Guo, SD Hall, LM Rocha, and L Li. 2009. “Literature Mining on Pharmacokinetics Numerical Data: A Feasibility Study," Journal of Biomedical Informatics, 42(4), pp. 726-735.
- S Kim, SD Hall, and L Li. 2009. “ A Novel Gibbs Maximum a Posteriori (GMAP) Methods on Bayesian Nonlinear Mixed-Effects Pharmacokinetic (PK) Models," Journal of Biopharmaceutical Statistics, 19, pp. 700-720.
- J Zhou, Z Qin, S Kim, Z Wang, M Yu, SD Hall, and L Li. 2009. “Drug-drug interaction prediction assessment," Journal of Biopharmaceutical Statistics, 19(4), pp. 641-657.
- M Yu, S Kim, Z Wang, SD Hall, and L Li. 2008. “A Bayesian meta-analysis on published sample mean and variance pharmacokinetic data with application to Drug-Drug Interaction prediction," Journal of Biopharmaceutical Statistics, 18(6), pp. 1063-1083.

- S-H Kim and S-H Kim. 2006. “A Divide-and-Conquer approach in Applying EM for Large Recursive Models with Incomplete Categorical Data," Computational Statistics & Data Analysis, 50(3), pp. 611-641.
- S-H Kim and S-H Kim. 2006. “A note on collapsibility in recursive graphical models of contingency tables," Scandinavian Journal of Statistics, 33(3), pp. 575-590.
- S-H Kim and S-H Kim. 2005. “Fluctuation of Estimates in an EM Procedure for Categorical Data," Journal of Statistical Computation and Simulation, 75(12), pp. 941-957.
- S-H Kim and S-H Kim. 2004. “Two Conditions for Modelling Large Bayesian Networks," in Proceedings of 23rd IASTED International Conference, Modelling, Identification, and Control. pp. 529-534, Grindelwald, Switzerland.
- S-H Kim and S-H Kim. 2003. “Fluctuation of Estimates in an EM Procedure," in Proceedings of the Spring Conference of Korean Statistical Society, pp. 293-298, Cheju, Korea.
- S-H Kim and S-H Kim. 2002. “Conditions for Hyper-EM and Large Graphical Modeling," in Proceedings of the Autumn Conference of Korean Statistical Society, pp. 293-298, Chuncheon, Korea.
- S-H Kim and S-H Kim. 2002. “D-Splitting And Hyper-EM For Large Bayesian Networks Of Categorical Variables," The 6th World Multiconference on Systemics, Cybernetics and Informatics, pp. 360-365, Orlando, Florida.

- C Warden, S-H Kim, and SV Yi. 2008. “The Evolutionary Impact of Functional RNA Secondary Structures with Protein-Coding Regions in Yeast," PLoS One, 3(2), pp. e1559.
- S-H Kim and SV Yi. 2008. “Mammalian nonsynonymous sites are not overdispersed comparative genomic analysis of index of dispersion of mammalian proteins," Molecular Biology and Evolution, 25(2), pp. 634-642.
- N Elango, S-H Kim, NISC Comparative Sequencing Group, and SV Yi. 2008. “Mutations of different molecular origins exhibit contrasting patterns of regional substitution rate variation," PLoS Computational Biology, 4(2), pp. e1000015.
- S-H Kim and SV Yi. 2007. “Understanding the relationship between sequence and functional evolution in yeast proteins," Genetica, 131(2), pp. 151-156.
- S-H Kim, N Elango, C Warden, E Vigoda, and SV Yi. 2006. “Heterogeneous genomic molecular clocks in primates," PLoS Genetics, 2(10), pp. 1527-1534 (e163).
- S-H Kim and S. V. Yi. 2006. “Correlated asymmetry of sequence and functional divergence between duplicate proteins of Saccharomyces cerevisiae," Molecular Biology and Evolution, 23(5), pp. 1068-1075.

- Datta S, Datta S, Kim S, Chakraborty S, and Gill R. 2010. “Statistical analysis of next generation sequence data: A partial overview,” Journal of Proteomics & Bioinformatics, 3, pp. 183-190.
- D. H. Kim, S. H. Kim, K. H. Kwon, and X. Li. 2002. “Best Polynomial Approximation in Sobolev-Laguerre and Sobolev-Legendre Spaces," Constructive approximation, 18, pp. 551-568.
- R. M. Kil, Y. Kim, H. Kim, S. Kim, and S. Kim. 2000. “A Design of Noise-Robust Speech-Front-End Based on Tree-Structured Filter-Bank," International Conference on Neural Information Processing, 1:112-117, Daejeon, Korea.
- D. H. Kim, S. H. Kim, and K. H. Kwon. 2000. “Best polynomial approximation in Sobolev-Laguerre space," in Proceedings of the Autumn Conference of the Korean Mathematical Society, Seoul, Korea.