Curriculum vita
Baolin Wu
June 2014
Contact Information
Address
Phone
Fax
Email
Division of Biostatistics
School of Public Health, University of Minnesota
A460 Mayo Building, MMC 303
420 Delaware St SE
Minneapolis, MN 55455
(612) 624-0647
(612) 626-0660
baolin@umn.edu
Education
1999-2004
1995-1999
Ph.D. in Biostatistics, Yale University, New Haven, CT.
B.S. in Probability and Statistics, Peking University, Beijing, P.R.China.
Positions
2010-Present
2004-2010
Tenured Associate Professor, Division of Biostatistics, School of Public
Health, University of Minnesota
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; Biometrical 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 Statistics; Journal of Biological Systems; Journal of Biomedicine and Biotechnology; Journal of
the American Statistical Association; Nucleic Acids Research; Physiological Genomics; Statistical 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 Computational 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 differential 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, SpringerVerlag, 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, PanoskaltsisMortari 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 detection. 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: 17351744.
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, PanoskaltsisMortari 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: 17561758.
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 Proteomics 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. Proceedings 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. American 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 enrichment 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
Advisee/Mentee
Tina Gunderson
Bo Peng
Wei Zhang
Erin Austin
Erin Austin
Tingting Zhao
Sun Kyung Kim
Shuzhen Li
Xiaowiao Wei
Wei Zhang
Ze Tian
Byeran Hwang
Shuzhen Li
Tingting Zhao
Guobin Zhao
Jiaqi Yang
Xiting Cao
Yanni Zhu
Fang Liu
Wei Zhong
Lijuan Shen
Shuzhen Li
Yi Peng
Degree
program
MS
PhD
PhD
PhD
PhD
MS
PhD
PhD
PhD
PhD
PhD
MS
PhD
MS
MS
MS
MS
PhD
MS
MS
MS
PhD
MS
Feng Tai
Pei Li
Kejia Shan
Song Liu
Seongho Wu
Eshrat Emamian
Jia Hui
PhD
MS
PhD
PhD
PhD
PhD
PhD
Lu Le
PhD
James Pattola
Meng Zhao
Jiaqi Yang
Yanni Zhu
MS
PhD
PhD
PhD
Major
Biostatistics
Statistics
Computer Science
Biostatistics
Biostatistics
Biostatistics
Biostatistics
Biostatistics
Statistics
Computer Science
Computer Science
Computer Science
Biostatistics
Biostatistics
Biostatistics
Biostatistics
Biostatistics
Biostatistics
Biostatistics
Biostatistics
Biostatistics
Biostatistics
Biostatistics
Biostatistics
Biostatistics
Statistics
Statistics
Statistics
Oral Biology
Biological Sciences
Nanyang Technological
University, Singapore
Biological Sciences
Nanyang Technological
University, Singapore
Biostatistics
Applied Economics
Mathematics
Biostatistics
7
Date of
Completion
2014
2014
2014
2014
2013
2013
2012
2012
2012
2011
2010
2009
2009
2011-2013
20082008
2008
2008
2007
2007
2007
2007
2007
2007
2007
2007
2007
2007
2007
2007
Mentor
roles
Exam committee member
Exam committee member
Exam committee member
Exam committee member
PhD oral exam committee member
Exam committee member
exam committee member
Defense member
Exam committee member
Exam committee member
Exam committee member
Exam committee member
Exam committee member
Academic advisor
Academic advisor
Plan B advisor
Plan B advisor
Exam committee member
Plan B advisor
Academic advisor
Academic advisor
Academic advisor
Academic advisor
Exam committee member
Exam committee member
Exam committee member
Exam committee member
Exam committee member
Exam committee member
Exam committee member
Dissertation reader
2007
Dissertation reader
2006
2006
2006
2006
Exam committee member
Exam committee member
Exam committee member
Academic advisor