Curriculum vita

Baolin Wu June 2014

Contact Information

Address Division of Biostatistics School of Public Health, University of Minnesota A460 Mayo Building, MMC 303 420 Delaware St SE Minneapolis, MN 55455 Phone (612) 624-0647 Fax (612) 626-0660 Email [email protected]

Education

1999-2004 Ph.D. in Biostatistics, Yale University, New Haven, CT. 1995-1999 B.S. in Probability and Statistics, Peking University, Beijing, P.R.China.

Positions

2010-Present Tenured Associate Professor, Division of Biostatistics, School of Public Health, University of Minnesota 2004-2010 Tenure-track Assistant Professor, Division of Biostatistics, School of Public Health, University of Minnesota

Student Advising

• Wei Zhang (ongoing CS PhD): co-advisor.

• Xiting Cao (PhD): graduated November 2011 and now worked for Merck.

• Ran Li (PhD): graduated December 2011 and now worked for Abbott.

• Sang Mee Lee (PhD): graduated July 2011 and now a Research Assistant Professor of Biostatistics at Department of Health Studies, University of Chicago. Won the student paper award at the 2010 ENAR meeting.

• Fang Liu (MS): graduated May 2007 and now worked for UnitedHealth.

• Jiaqi Yang (MS): graduated May 2008 and now worked for Schlumberger-Doll Research.

1 Professional Service

Referee for journals

Annals of Applied Statistics; Applied Statistics; Behavior Genetics; Bioinformatics; Biomet- rical Journal; Biometrics; Biometrika; Biostatistics; BMC Bioinformatics; Communications in Statistics - Simulation and Computation; Computational Statistics and Data Analysis; Genome Biology; IEEE/ACM Transactions on Computational Biology and Bioinformatics; Journal of Agricultural, Biological, and Environmental Statistics; Journal of Applied Statis- tics; Journal of Biological Systems; Journal of Biomedicine and Biotechnology; Journal of the American Statistical Association; Nucleic Acids Research; Physiological Genomics; Sta- tistical Applications in Genetics and Molecular Biology; Statistics in Biopharmaceutical Research; Statistics in Medicine; Statistica Sinica; Technometrics; Test.

Grant review

1. NCI study section for RFA CA 07-005 “Advanced Proteomic Platforms and Compu- tational Sciences for the NCI Clinical Proteomic Technologies Initiative”. 2006.

2. Review grant applications for Italian Ministry of Health in association with NIH. 2009.

3. Review grant applications for NIH. 2009-2010.

UofM Services and Committees

1. Exam Committee, 2009- (PhD exam chair for 2012-).

2. Admission Committee, 2004-2005.

3. Seminar Committee, 2004 - 2010.

4. Faculty Search Committee, 2005 - 2006. 2007 - 2010.

5. School of Public Health APT Ad Hoc Committee, 2009.

6. School of Public Health Research Committee, 2008 - 2010.

2 Research Articles

1. Zhao H, Wu B, Sun N (2003). DNA-protein binding and gene expression patterns. In Goldstein DR(ed). Science and Statistics: A Festschrift for Terry Speed. IMS Lecture Notes-Monograph Series, 40: 259-274.

2. Wu B, Abbott T, Fishman D, Mcmurrary W, Mor G, Stone K, Ward D, Williams K, Zhao H (2003). Comparison of statistical methods for classification of ovarian cancer using a proteomics dataset. Bioinformatics, 19: 1636-1643.

3. Goh C, Lan N, Douglas S, Wu B, Bertone P, Echols N, Milburn D, Montelione G, Zhao H, Gerstein M (2003). Mining the structural genomics pipeline: Identification and analysis of protein properties that affect high-throughput experimental analysis. Journal of Molecular Biology, 336: 115-30.

4. Lai Y, Wu B, Chen L, and Zhao H (2004). Statistical method for identifying differ- ential gene-gene coexpression patterns. Bioinformatics, 20: 3146-3155.

5. Lin N, Wu B, Jansen R, Gerstein M, Zhao H (2004). Information assessment on predicting protein-protein interactions. BMC Bioinformatics, 5:154.

6. Carriero N, Osier M, Cheung K, Miller P, Gerstein M, Zhao H, Wu B, Rifkin S, Chang J, Zhang H, White K, Williams K, Schultz M (2005). A “high productivity/low maintenance” approach to high performance computation for biomedicine: Four case studies. Journal of American Medical Informatics Association, 12: 90-98.

7. Gulcicek E, Colangelo C, McMurray W, Stone K, Wu B, Wu T, Spratt H, Kurosky A, Zhao H, Williams K (2005). Proteomics and the analysis of proteomic data. In Davison D, Page R, Petsko G, Stormo G, and Stein L(ed). Current Protocols in Bioinformatics, John Wiley and Sons, Indianapolis, IN.

8. Huang T, Wu B, Lizardi P, Zhao H (2005). Detection of DNA copy number alterations using penalized least squares regression. Bioinformatics, 21: 3811-3817.

9. Wu B (2005). Differential gene expression detection using penalized linear regression model: the improved SAM statistics. Bioinformatics, 21: 1565-1571.

10. Yu W, Wu B, Huang T, Li X, Williams K, Zhao H (2006). Statistical methods in proteomics. In Pham H(ed). Springer Handbook of Engineering Statistics, Springer- Verlag, London, UK.

11. Yu W, Wu B, Liu J, Li X, Williams K, Zhao H (2006). MALDI-MS data analysis for disease biomarker discovery. Methods in Molecular Biology, 328: 199-216.

12. Yu W, Wu B, Lin N, Stone K, Williams K, Zhao H (2006). Detecting and aligning peaks in mass spectrometry data with applications to MALDI. Computational Biology and Chemistry, 30: 27-38.

3 13. Yu W, Li X, Liu J, Wu B, Williams K and Zhao H (2006). Multiple peak alignment in sequential data analysis: A scale-space based approach. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 3: 208-219. 14. Wu B, Abbott T, Fishman D, McMurray W, Mor G, Stone K, Ward D, Williams K, Zhao H (2006). Ovarian cancer classification based on mass spectrometry analysis of sera. Cancer Informatics, 2: 123-132. 15. Wu B, Guan Z, and Zhao H (2006). Parametric and nonparametric FDR estimation revisited. Biometrics, 62: 735-744. 16. Wu B (2006). Differential gene expression detection and sample classification using penalized linear regression models. Bioinformatics, 22: 472-476. 17. Wu B, Liu N, Zhao H (2006). PSMIX: an R package for population structure inference via maximum likelihood method. BMC Bioinformatics, 7:317. 18. Oetting W, Wu B, Lande J, Brott M and Matas A (2006). Identification of DNA variants and genetic profiling of kidney allograft recipients using a custom SNP chip. Transplantation, 82(1 Suppl 2):911. 19. Whitson B, D’Cunha J, Hoang C, Wu B, Ikramuddin S, Buchwald H, Panoskaltsis- Mortari A, Kratzke R, Miller J and Maddaus M (2007). Comparison of minimally invasive vs open roux-en-y gastric bypass on immune effector cell function. Journal of the American College of Surgeons, 205(3 Suppl 1):S13. 20. Li N, Wu B, Wei P, Xie B, Xie Y, Xiao G and Pan W (2007). Functional group based linkage analysis of gene expression trait loci. BMC Proceedings 2007, 1(Suppl 1):S117. 21. Wu B (2007). Cancer outlier differential gene expression detection. Biostatistics, 8: 566-575. (To 50 most cited papers in Biostatistics up to April, 2012) 22. Liu F and Wu B (2007). Multi-group cancer outlier differential gene expression de- tection. Computational Biology and Chemistry, 31: 65-71. 23. Liu J, Yu W, Wu B and Zhao H (2008). Bayesian mass spectra peak alignment from mass charge ratios. Cancer Informatics, 4, 217-241. 24. Chen W, Kumar A, Hudson W, Li Q, Wu B, Staggs R, Lund E, Sam T and Kersey J (2008). Malignant transformation initiated by Mll-AF9: Gene dosage and critical target cells. Cancer Cell, 13, 432-440. 25. Guan Z, Wu B, and Zhao H (2008). Application of Bernstein polynomial in the estimation of false-discovery-rate. Statistica Sinica, 18: 905-923. 26. Fu S, Kodl M, Joseph A, Hatsukami D, Johnson E, Breslau N, Wu B, Bierut L (2008). Racial/Ethnic Disparities in the Use of Nicotine Replacement Therapy and Quit Ratios in Lifetime Smokers Aged 25-44. Cancer Epidemiology, Biomarkers & Prevention, 17: 1640-1647.

4 27. John C, Bangirana P, Byarugaba J, Opika-Opoka R, Idro R, Jurek A, Wu B, Boivin M (2008). Long-term cognitive impairment in children with cerebral malaria. Pediatrics, 122: e92-e99.

28. Whitson B, D’Cunha J, Andrade R, Kelly R, Groth S, Wu B, Miller J, Kratzke R and Maddaus M (2008). Thoracoscopic vs. thoracotomy approaches to lobectomy: differential impairment of cellular immunity. Annals of Thoracic Surgery, 86: 1735- 1744.

29. Hwang T, Sicotte H, Tian Z, Wu B, Kocher J, Wigle D, Kumar V and Kuang R (2008). Robust and efficient identification of biomarkers by classifying features on graphs. Bioinformatics, 24: 2023-2029.

30. Whitson B, DCunha J, Hoang C, Wu B, Ikramuddin S, Buchwald H, Panoskaltsis- Mortari A, Kratzke R, Miller J and Maddaus M (2009). Minimally invasive versus open roux-en-y gastric bypass: impact on immune effector cells. Surgery for Obesity and Related Diseases, 5: 181-193.

31. Kumar A, Li Q, Hudson W, Chen W, Sam T, Yao Q, Lund E, Wu B, Kowal B and Kersey J (2009). A role for MEIS1 in MLL-fusion gene leukemia. Blood, 113: 1756- 1758.

32. de Jong E, Xie H, Onsongo G, Stone M, Chen X, Kooren J, Refsland W, Griffin R, Ondrey F, Wu B, Le C, Rhodus N, Carlis J and Griffin T (2010). Quantitative Pro- teomics Reveals Myosin and Actin as Promising Saliva Biomarkers for Distinguishing Pre-Malignant and Malignant Oral Lesions. PLoS ONE, 5(6): e1114.

33. Kumar A, Sarver A, Wu B and Kersey J (2010). Meis1 maintains stemness signature in MLL-AF9 leukemia. Blood, 115: 3642-3643.

34. Canales, B.K., L. Anderson, L. Higgins, K. Ensrud-Bowlin, K.P. Roberts, Wu B, I.W. Kim, and M. Monga (2010). Proteome of Human Calcium Kidney Stones. Urology, 76(4): 1017.e13–1017.e20.

35. Onsongo, G., M.D. Stone, S.K. Van Riper, J. Chilton, Wu B, L. Higgins, T.C. Lund, J.V. Carlis, and T.J. Griffin (2010). LTQ-iQuant: A Freely Available Software Pipeline for Automated and Accurate Protein Quantification of Isobaric Tagged Peptide Data from LTQ Instruments. Proteomics, 10(19): 3533–3538.

36. Zhang W, Hwang B, Wu B, and Kuang R (2010). Network Propagation Models for Gene Selection. Proc. of IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS), 1–4.

37. Lai Y, Wu B, and Zhao H (2011). A permutation test approach to the choice of size k for the nearest neighbors classifier. Journal of Applied Statistics, 38(10): 2289-2302.

38. Li R, and Wu B (2012). Sparse regularized discriminant analysis of microarrays. Computational biology and chemistry, 39:14–19.

5 39. Zhang W, Johnson N, Wu B, and Kuang R (2012). Signed Network Propagation for Detecting Differential Gene Expressions and DNA Copy Number Variations. Proceed- ings of the ACM Conference on Bioinformatics, Computational Biology and Biomedicine, 337-344. doi:10.1145/2382936.2382979

40. Cao X, Wu B and Hertz MI (2013). Empirical null distribution based modeling of multi-class differential gene expression detection. Journal of Applied Statistics, 40(2):347-357.

41. Wu B (2013). Sparse cluster analysis of large-scale discrete variables with application to single nucleotide polymorphism data. Journal of Applied Statistics, 40(2):358-367.

42. Wu B (2013). On the geometric approach to empirical null distribution estimation for empirical Bayes modeling of multiple hypothesis testing. Computational biology and chemistry, 43:17-22.

43. Yang J, Zhang W, Wu B (2013). A note on statistical method for genotype calling of high-throughput SNP arrays. Journal of Applied Statistics, 40(6):1372-1381.

44. Bhargava M, ··· , Wu B, ··· , Wendt C (2013). Bronchoalveoalr Lavage Fluid Protein Profiling In ARDS: Early Differences Between Survivors And Non-Survivors. American Journal of Respiratory and Critical Care Medicine, 187:A2362.

45. Zhang W, Ota T, Shridhar V, Chien J, Wu B, Kuang R (2013). Network-based Survival Analysis Reveals Subnetwork Signatures for Predicting Outcomes of Ovarian Cancer Treatment. PLoS computational biology, 9(3):e1002975.

46. Bhargava M, ··· , Wu B, Lee SM, ··· , Wendt C (2013). Protein Expression Profile of Rat Type Two Alveolar Epithelial Cells During Hyperoxic Stress and Recovery. Amer- ican Journal of Physiology - Lung Cellular and Molecular Physiology, 305(9):L604-14.

47. Lee S, Wu B, and Kersey JH (2014). Statistical methods for one-sided gene set enrich- ment analysis. Computational biology and chemistry, accepted with minor revision.

48. Lee S, Wu B, and Kersey JH (2014). Likelihood based approach to gene set enrichment analysis with a finite mixture model. Statistics in Biosciences, 6(1), 38-54.

6 Student mentoring

Degree Date of Mentor Advisee/Mentee program Major Completion roles Tina Gunderson MS Biostatistics 2014 Exam committee member Bo Peng PhD Statistics 2014 Exam committee member Wei Zhang PhD Computer Science 2014 Exam committee member Erin Austin PhD Biostatistics 2014 Exam committee member Erin Austin PhD Biostatistics 2013 PhD oral exam committee member Tingting Zhao MS Biostatistics 2013 Exam committee member Sun Kyung Kim PhD Biostatistics 2012 exam committee member Shuzhen Li PhD Biostatistics 2012 Defense member Xiaowiao Wei PhD Statistics 2012 Exam committee member Wei Zhang PhD Computer Science 2011 Exam committee member Ze Tian PhD Computer Science 2010 Exam committee member Byeran Hwang MS Computer Science 2009 Exam committee member Shuzhen Li PhD Biostatistics 2009 Exam committee member Tingting Zhao MS Biostatistics 2011-2013 Academic advisor Guobin Zhao MS Biostatistics 2008- Academic advisor Jiaqi Yang MS Biostatistics 2008 Plan B advisor Xiting Cao MS Biostatistics 2008 Plan B advisor Yanni Zhu PhD Biostatistics 2008 Exam committee member Fang Liu MS Biostatistics 2007 Plan B advisor Wei Zhong MS Biostatistics 2007 Academic advisor Lijuan Shen MS Biostatistics 2007 Academic advisor Shuzhen Li PhD Biostatistics 2007 Academic advisor Yi Peng MS Biostatistics 2007 Academic advisor Exam committee member Feng Tai PhD Biostatistics 2007 Exam committee member Pei Li MS Biostatistics 2007 Exam committee member Kejia Shan PhD Statistics 2007 Exam committee member Song Liu PhD Statistics 2007 Exam committee member Seongho Wu PhD Statistics 2007 Exam committee member Eshrat Emamian PhD Oral Biology 2007 Exam committee member Jia Hui PhD Biological Sciences 2007 Dissertation reader Nanyang Technological University, Singapore Lu Le PhD Biological Sciences 2007 Dissertation reader Nanyang Technological University, Singapore James Pattola MS Biostatistics 2006 Exam committee member Meng Zhao PhD Applied Economics 2006 Exam committee member Jiaqi Yang PhD Mathematics 2006 Exam committee member Yanni Zhu PhD Biostatistics 2006 Academic advisor

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