Cumulative BioBibliography University of California, Santa Cruz September 12, 2016

Transcription

1 Cumulative BioBibliography University of California, Santa Cruz September 12, 2016 Ju Hee Lee Assistant Professor Department of Applied Mathematics and Statistics School of Engineering 1

2 EMPLOYMENT HISTORY Date Title Institution present Assistant Professor Applied Mathematics and Statistics, UCSC Visiting Assistant Professor Statistics, The Ohio State University Postdoctoral Fellow Biostatistics, UT M.D. Anderson Cancer Center Graduate Research Assistant Statistics, The Ohio State University 2007 Graduate Student Consultant Statistical Consulting Service, The Ohio State University Graduate Teaching Assistant Statistics, The Ohio State University EDUCATION Date Degree Institution 2010 Ph.D., Statistics The Ohio State University 2006 Master of Sciences, Statistics The Ohio State University 1999 Bachelor of Science, Statistics Ewha Womans University, Seoul, Korea HONORS AND AWARDS Date Honor/Award 2015 Selected for the 2015 JSM promotional project: Bayesian Models for Heterogeneity in Human Cancers ( pressreleases/jsm2015-heterogeneityinhumancancers.pdf), ScienceDaily ( among many others Selected for the 2015 JSM promotional project: Bayesian Dose-Finding in Two Treatment Cycles Based on the Joint Utility of Efficacy and Toxicity ( amstat.org/newsroom/pressreleases/jsm2015-two-cycledose-findingmethod.pdf), ScienceDaily ( among many others Travel award to the ENAR Workshop for Junior Researchers, ENAR 2009 Whitney Award for Research, Dept. of Statistics, The Ohio State University 2008, 2009 Travel award to JSM, Dept. of Statistics, The Ohio State University SCHOLARLY AND CREATIVE WORK A. Contributions to Books 3. Lee, J., Müller, P., Sengupta, S., Gulukota, K., and Ji, Y. (2016) Bayesian Feature Allocation Models for Tumor Heterogeneity. Statistical Analysis for High-Dimensional Data, A. Frigessi et al. (eds.), Abel Symposia, Springer 2

3 2. Lee, J., Müller, P., Zhu, Y. and Ji, Y. (2015) A Nonparametric Bayesian Model for Nested Clustering. Statistical Planning and Analysis in Proteomics, Jung K.(eds), Springer 1. Ji, Y., Sengupta, S., Lee, J., Müller, P., and Gulutoka, K. (2015). Estimating latent cell subpopulations with Bayesian feature allocation models. in Nonparametric Bayesian Methods in Biostatistics and Bioinformatics, Mitra, R. and Müller, P. (eds), Springer-Verlag. B. Journal Articles 14. Lee, J., Müller, P., Sengupta, S., Ji, Y. and Gulukota, K. (2016) Bayesian Inference for Intra-Tumor Heterogeneity in Mutations and Copy Number Variation. Journal of the Royal Statistical Society: Series C (Applied Statistics), 65 (4), Lee, J., Thall, P. F., Ji, Y. and Müller, P. (2016) A Decision-Theoretic Phase I-II Design for Ordinal Outcomes in Two Cycles. Biostatistics, 17 (2), Lee, J., Müller, P., Ji, Y. and Gulukota, K. (2015) A Bayesian Feature Allocation Model for Tumor Heterogeneity. The Annals of Applied Statistics, 9 (2), Lee, J., Thall, P. F., Ji, Y. and Müller, P. (2015) Bayesian Adaptive Dose Selection in Multiple Treatment Cycles Based on the Joint Utility of Toxicity and Efficacy. Journal of the American Statistics Association, 110 (510), Lee, J. and MacEachern, S. N. (2014) Inference Functions in High Dimensional Bayesian Inference. Statistics and Its Interface, 7 (4), Lee, J., MacEachern, S. N., Lu, Y. and Mills, G. B. (2014) Local-Mass Preserving Prior Distribution for Nonparameteric Bayesian Models. Bayesian Analysis, 9 (2), Lee, J., Ji, Y., Liang, S., Cai, G. and Müller, P. (2013) Bayesian Hierarchical Model for Differential Gene Expression Using RNA-seq Data. Statistics in Biosciences, 7 (1), Xu, Y., Lee, J., Yuan, Y., Mitra, R., Shoudan, L., Müller, P. and Ji, Y. (2013) Nonparametric Bayesian Bi-Clustering for Next Generation Sequencing Count Data. Bayesian Analysis, 8 (4), Lee, J., Müller, P., Zhu, Y. and Ji, Y. (2013) A Nonparametric Bayesian Model for Local Clustering with Application to Proteomics. Journal of the American Statistics Association, 108 (503), Cai, G., Li, H. Lu, Y., Lee, J., Müller, P., Ji, Y. and Liang, S. (2012) Accuracy of RNA-Seq and Its Dependence on Sequencing Depth. BMC Bioinformatics, 13 (Suppl 13) 4. Hans, C., Allenby, G. M., Craigmile, P. F., Lee, J., MacEachern, S. N. and Xu, X. (2012) Covariance Decompositions for Accurate Computation in Bayesian Scale-Usage Model. Journal of Computational and Graphical Statistics, 21 (2), Lee, J., Ji, Y., Liang, S., Cai, G. and Müller, P. (2011) On Differential Gene Expression Using RNA- seq Data. Cancer Informatics, 10,

4 2. Lee, J. and MacEachern, S. N. (2011) Consistency of Bayes Estimators without the Assumption that the Model is Correct. Journal of Statistical Planning and Inference, 141 (2), Bush, C., Lee, J. and MacEachern, S. N. (2010) Minimally Informative Prior Distributions for Non- parametric Bayesian Analysis. Journal of the Royal Statistical Society: Series B (Statistical Methodology), 72 (2), C. Critical Reviews written for others 2. Review Statistical Methods in Biology. S.J. Welham, S.A. Gezan, S.J. Clark and A. Mead (CRC Press) in Journal of Agricultural, Biological, and Environmental Statistics (2015) 1. Lee, J. (2014) Discussion on Robust Bayesian Graphical Modeling Using Dirichlet t-distributions by Michael Finegold and Mathias Drton. Bayesian Analysis 9 (3), D. Papers in Conference Proceedings 1. Sengupta, S., Guluokta, K., Lee, J., Müller, P., and Ji, Y. (2015) Bayclone: Bayesian Nonparametric Inference of Tumor Subclones Using NGS Data. In Proceedings of The Pacific Symposium on Biocomputing (PSB) 2015, 20: E. Other Publications 1. BayClone2: Bayesian Feature Allocation Model for Tumor Heterogeneity (R package) released in December,

5 PROFESSIONAL ACTIVITIES Papers Presented at Professional Meetings Jun 2016 BayClone3: Characterizing Subclonal Structure in Tumors Using NGS Data The ISBA 2016 World Meeting, Sardinia, Italy PEER REVIEWED, INVITED A Bayesian Feature Allocation Model for Intra-Tumor Heterogeneity in Mutations and Copy Number Variation Dec 2015 The 8th International Conference of the ERCIM WG on Computational and Methodological Statistics (ERCIM 2015), London, UK PEER REVIEWED, INVITED Jun 2015 The 10th Conference on Bayesian Nonparametrics, Raleigh, NC CON- TRIBUTED Aug 2015 Aug 2014 Jul 2014 Jun 2014 Mar 2013 Jun 2012 Apr 2012 Jun 2011 Mar 2011 Jun 2011 Aug 2010 Bayesian Dose-Finding in Two Treatment Cycles Based on the Joint Utility of Efficacy and Toxicity Joint Statistical Meetings, Seattle, WA PEER REVIEWED, INVITED A Bayesian Feature Allocation Model for Tumor Heterogeneity Joint Statistical Meetings, Boston, MA TOPIC-CONTRIBUTED The ISBA 2014 World Meeting, Cancun, Mexico ICSA and KISS Joint Applied Statistics Symposium, Portland, OR A Nonparametric Bayesian Model for Local Clustering Eastern North America Region: Meetings, Orlando, FL PEER REVIEWED, INVITED Western North America Region Meetings, Fort Collins, CO PEER RE- VIEWED, INVITED Eastern North America Region: Meetings, Washington D.C. CONTRIBUTED Bayesian Hierarchical Model for Differential Gene Expression Using RNA-seq Data Western North America Region Meetings, San Louis Obispo, CA PEER RE- VIEWED, INVITED On Differential Gene Expression Using RNA-seq Data Eastern North America Region: Meetings, Miami, FL CONTRIBUTED Local-Mass Preserving Prior Distribution for Nonparameteric Bayesian Models The 8th Workshop on Bayesian Nonparametrics, Veracruz, Mexico CON- TRIBUTED Joint Statistical Meetings, Vancouver, B.C. Canada CONTRIBUTED 5

6 Aug 2009 Aug 2008 The Head and Tail Models Joint Statistical Meetings, Washington, D.C. CONTRIBUTED Minimally Informative Nonparametric Bayesian Analysis Joint Statistical Meetings, Denver, CO CONTRIBUTED Memberships or Activities in Professional Associations (2016) Treasurer, Bayesian Nonparametrics Section of ISBA (2015) Member of the Mitchell Prize committee for ISBA meetings 2016 (2015) Organizer of invited session on Bayesian Variable Selection for Complex and High-Dimensional Data for 2015 Joint Statistical Meetings (JSM), Seattle, WA (2014) Organizer of invited session on Bayesian Models for High Dimensional Complex Data for 2014 ICSA and KISS Joint Applied Statistics Symposium, Portland, OR (2014) Reviewer for the Section on Bayesian Statistical Science (SBSS) sponsored student paper competition for JSM 2014 (2013) Member of the SBSS Nominating Committee (2011-present) Member of the American Statistical Association (ASA). (2010-present) Member of the International Society for Bayesian Analysis (ISBA). 6

7 Talks and Presentations at Colleges and Universities A Bayesian Feature Allocation Model for Intra-Tumor Heterogeneity in Mutations and Copy Number Variation Mar 2016 Mar 2016 Mar 2016 Dec 2015 Sep 2015 Nov 2014 Department of Biostatistics, Columbia University, New York, New York Department of Mathematical Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Korea Department of Statistics, Ewha Womans University, Seoul, Korea Seminars in Statistics, Collegio Carlo Alberto, Turin, Italy Department of Biostatistics, UC San Francisco, San Francisco, CA Department of Biomolecular Engineering, UC Santa Cruz, Santa Cruz, CA A Nonparametric Bayesian Model for Local Clustering Feb 2013 Feb 2013 Feb 2013 Oct 2012 Feb 2012 Nov 2011 Department of Applied Mathematics and Statistics, UC Santa Cruz, Santa Cruz, CA Department of Biostatistics, Indiana University, Indianapolis, IN Department of Biostatistics and Epidemiology, Cleveland Clinic, Cleveland, OH Statistics and Biostatistics Seminars, The Ohio State University, Columbus, OH Department of Statistics, University of Connecticut, Storrs, CT BCB Weekly Seminar Series, U.T. M.D. Anderson Cancer Center, Houston, TX Bayesian Hierarchical Model for Differential Gene Expression Using RNA-seq Data Feb 2012 Feb 2012 Center for Health, Intervention, and Prevention, University of Connecticut, Storrs, CT Department of Statistics, Purdue University, West Lafayette, IN On Differential Gene Expression Using RNA-seq Data Feb 2011 Department of Mathematical Science, University of Cincinnati, Cincinnati, OH A Minimally Informative Nonparametric Bayesian Analysis Feb 2010 Feb 2010 Mar 2009 Department of Bioinformatics and Computational Biology, U.T. M.D. Anderson Cancer Center, Houston, TX Department of Mathematical Science, University of Cincinnati, Cincinnati, OH Statistics and Biostatistics Seminars, The Ohio State University, Columbus, OH 7

8 Scale Usage Models May 2008 Research seminar in Statistics, Psychology, and Marketing, The Ohio State University, Columbus, OH Participation in Research Programs The 2013 ENAR Workshop for Junior Investigators (March 2013) Summer research program on Semiparametric Bayesian Inference: Applications in Pharmacokinetics and Pharmacodynamics in the Statistical and Applied Mathematical Sciences Institute (July 2010) 8