Papers by Subject Area

Gene expression data analysis

  1. Pan, W. (in press). ``Incorporating Gene Functional Annotations in Detecting Differential Gene Expression". To appear Applied Statistics.
  2. Xie, Y., Pan, W., Khodursky, A. (in press). ``A note on using permutation based false discovery rate estimate to compare different analysis methods for microarray data". Bioinformatics. (Also Research Report 2005-013, Division of Biostatistics, University of Minnesota)
  3. Pan, W., Xiao G, Huang X (in press). ``Using Input Dependent Weights for Model Combination and Model Selection with Multiple Sources of Data". Statistica Sinica, a special issue on Machine Learning. (Also Research Report 2004-029, Division of Biostatistics, University of Minnesota)
  4. Xiao, G. and Pan, W. (in press). ``Gene Function Prediction by a Combined Analysis of Gene Expression Data and Protein-Protein Interaction Data". Journal of Bioinformatics and Computational Biology. (Also Research Report 2004-026, Division of Biostatistics, University of Minnesota)
  5. Huang, X., Pan, W., Grindle, S., Han, X., Chen, Y., Park, S.J., Miller, L.M., Hall, J. (2005). ``A comparative study of discriminating human heart failure etiology using gene expression profiles". BMC Bioinformatics, 6: 205. (Also Research Report 2004-023, Division of Biostatistics, University of Minnesota)
  6. Huang, X., Pan, W., Han, X., Chen, Y., Miller, L.W., Hall, J. (2005). ``Borrowing information from relevant microarray studies for sample classification using weighted partial least squares". Computational Biology and Chemistry, 29, 204-211. (Also Research Report 2004-024, Division of Biostatistics, University of Minnesota)
  7. Martinez-Vaz, B.M., Xie, Y., Pan, W., Khodursky, A.B. (2005) ``Genome-wide localization of mobile elements: experimental, statistical and biological considerations". BMC Genomics, 6: 81.
  8. Pan, W. (2005). ``Incorporating Biological Information as a Prior in an Empirical Bayes Approach to Analyzing Microarray Data". Statistical Applications in Genetics and Molecular Biology, 4(1), Article 12. (Also Research Report 2004-028, Division of Biostatistics, University of Minnesota)
  9. Guo, X. and Pan, W. (2005). ``Using weighted permutation scores to detect differential gene expression with microarray data". Journal of Bioinformatics and Computational Biology, 3, 989-1006. (Also Research Report 2004-022, Division of Biostatistics, University of Minnesota)
  10. Xie, Y., Jeong, K.S., Pan, W., Khodursky,A. and Carlin, B.P. (2004). "A case study on choosing normalization methods and test statistics for microarray data". Comparative and Functional Genomics, 5, 432-444. (Also Research Report 2003-016, Division of Biostatistics, University of Minnesota)
  11. Huang, X., Pan, W., Park, S., Han, X., Miller, L.W. and Hall, J. (2004). ``Modeling the relationship between LVAD support time and gene expression changes in the human heart by penalized partial least squares". Bioinformatics, 20, 888-894. (Also Research Report 2004-020, Division of Biostatistics, University of Minnesota)
  12. Huang, X. and Pan, W. (2003). "Linear regression and two-class classification with gene expression data". Bioinformatics, 19, 2072-2078. (Also Research Report 2003-005, Division of Biostatistics, University of Minnesota)
  13. Pan, W., Lin, J. and Le, C. (2003) ``A Mixture Model Approach to Detecting Differentially Expressed Genes with Microarray Data". Functional & Integrative Genomics, 3, 117-124. (Also Report 2003-004, Division of Biostatistics, University of Minnesota, 2003)
  14. Qi, H., Aguiar, D.J., Williams, S.M., La Pean, A., Pan, W. and Verfaillie, C.M. (2003). ``Idenitification of genes responsible for osteroblast differentiation from human mesodermal progenitor cells". Proceedings of National Academy of Science USA, 100, 3305-3310.
  15. Guo, X., Qi, H., Verfaillie, C.M. and Pan, W. (2003). ``Statistical significance analysis of longitudinal gene expression data". To appear in Bioinformatics. (Also Report 2003-001, Division of Biostatistics, University of Minnesota, 2003)
  16. Pan, W. (2003). ``On the use of permutation in and the performance of a class of nonparametric methods to detect differential gene expression". A shortened version appeared in Bioinformatics. 19, 1333-1340. and its PDF reprint. (Longer version: Report 2002-021, Division of Biostatistics, University of Minnesota, 2002)
  17. Zhao, Y. and Pan, W. (2002). ``Modified nonparametric approaches to detecting differentially expressed genes in replicated microarray experiments". A shortened version in Bioinformatics, 19, 1046-1054. (Also Report 2002-018, Division of Biostatistics, University of Minnesota, 2002)
  18. Lin J, Ozeki M, Javel E, Zhao Z, Pan W, Schlentz E, Levine S. (2003). ``Identification of gene expression profiles in rat ears with cDNA microarrays". Hear Res., 175, 2-13.
  19. Lin, J., Tsuboi, Y., Pan, W., Giebink, S.G. and Kim, Y. (2002). ``Analysis by cDNA Microarrays of Altered Gene Expression in Middle Ears of Rats Following Pneumococcal Infection". Int J Pediatr Otorhinolaryngol, 65, 203-211.
  20. Huang, X. and Pan, W. (2002) ``Comparing three methods for variance estimation with duplicated high density oligonucleotide arrays". Functional & Integrative Genomics, 2, 126-133. (Also Report 2002-014, Division of Biostatistics, University of Minnesota, 2002)
  21. Pan, W. (2002) ``A Comparative Review of Statistical Methods for Discovering Differentially Expressed Genes in Replicated Microarray Experiments". Bioinformatics, 12, 546-554. (Also Report 2001-028, Division of Biostatistics, University of Minnesota, 2001)
  22. Pan, W., Lin, J. and Le, C. (2002) ``How Many Replicates of Arrays Are Required to Detect Gene Expression Changes in Microarray Experiments? A Mixture Model Approach". GenomeBiology, /2002/3/5/research/0022.
    (Also Report 2001-012, Division of Biostatistics, University of Minnesota, 2001) (First issued July 2001, revised Dec 2001)
  23. Pan, W., Lin, J. and Le, C. (2002) ``Model-Based Cluster Analysis of Microarray Gene Expression Data". (Also Report 2001-027, Division of Biostatistics, University of Minnesota, 2001) (First issued Feb 2001; revised Nov 2001).
    GenomeBiology, /2002/3/2/research/0009.
    (pdf, Data).

Analysis of correlated data: Generalized linear models and GEE

  1. Guo, X., {\bf Pan, W.}, Connett, J.E., Hannan, P.J., French, S.A. (2005). ``Small-Sample Performance of the Robust Score Test and Its Modifications in Generalized Estimating Equations". To appear Statistics in Medicine. (Also Research Report 2004-021, Division of Biostatistics, University of Minnesota)
  2. Luan, X., {\bf Pan, W.}, Gerberich, S.G. and Carlin, B.P. (2005). ``Does it always help to adjust for misclassification of a binary outcome in logistic regression?" Statistics in Medicine, 24, 2221-2234.
  3. Pan, W. (2002) ``A Note on the Use of Marginal Likelihood and Conditional Likelihood in Analyzing Clustered Data". The American Statistician, 56, 171-174. (Also Report 2002-006, Division of Biostatistics, University of Minnesota, 2002)
  4. Pan, W. and Connett, J.E. (2002) ``Selecting the Working Correlation Structure in Generalized Estimating Equations with Application to the Lung Health Study". Statistica Sinica, 12, 475-490. (Also Report 2001-022, Division of Biostatistics, University of Minnesota, 2001)
  5. Pan, W. and Wall, M.M. (2002) ``Small-Sample Adjustments in Using the Sandwich Variance Estimator in Generalized Estimating Equations ". Statistics in Medicine, 21, 1429-1441. (Also Report 2001-015, Division of Biostatistics, University of Minnesota, 2001)
  6. Pan, W. (2002) ``Application of Conditional Moment Tests to Model Checking for Generalized Linear Models". Biostatistics, 3, 267-276. (Also Report 2001-009, Division of Biostatistics, University of Minnesota, 2001)
  7. Pan, W. (2002) ``Goodness-of-fit Tests for GEE with Correlated Binary Data". Scandinavian Journal of Statistics, 29, 101-110. (Also Report 2000-009, Division of Biostatistics, University of Minnesota, 2000)
  8. Pan, W. (2001) ``On the robust variance estimator in generalised estimating equations". Biometrika, 88, 901-906. (Also Report 2001-005, Division of Biostatistics, University of Minnesota, 2001)
  9. Pan, W. (2001) ``Sample Size and Power Calculations With Correlated Binary Data". Controlled Clinical Trials, 22, 211-227. (Also Report 2001-002, Division of Biostatistics, University of Minnesota, 2001)
  10. Pan, W., Connett, J.E., Porzio, G.C. and Weisberg, S. (2001) ``Graphical Model Checking with Correlated Response Data". Statistics in Medicine, 20, 2935-2949. (Also Report 2000-030, Division of Biostatistics, University of Minnesota, 2000)
  11. Pan, W. (2001) ``Model Selection in Estimating Equations". Biometrics, 57, 529-534. (Also Report 2000-028, Division of Biostatistics, University of Minnesota, 2000)
  12. Pan, W. (2001) ``Akaike's Information Criterion in Generalized Estimating Equations". Biometrics, 57, 120-125. (Also Report 2000-013, Division of Biostatistics, University of Minnesota, 2000)
  13. Pan, W. and Le, C.T. (2001) ``Bootstrap Model Selection in Generalized Linear Models". Journal of Agricultural, Biological and Environmental Statistics, 6, 49-61. (Also Report 2000-008, Division of Biostatistics, University of Minnesota, 2000)
  14. Pan, W., Connett, J.E. and Louis, T.A. (2000) ``A Note On Marginal Linear Regression With Correlated Response Data". The American Statistician, 54, 191-195. (Also Report 2000-006, Division of Biostatistics, University of Minnesota, 2000)

Survival analysis with interval censored data

  1. Pan, W. and Chappell, R. (2002) ``Estimation in the Cox Proportional Hazards Model with Left Truncated and Interval Censored Data". Biometrics, 58, 64-70. (Also Report 2001-021, Division of Biostatistics, University of Minnesota, 2001)
  2. Pan, W. (2001) ``A Multiple Imputation Approach to Regression Analysis for Doubly Censored Data with Application to AIDS Studies". Biometrics, 57, 1245-1250. (Also Report 2000-010, Division of Biostatistics, University of Minnesota, 2000)
  3. Pan, W. (2000) ``Smooth Estimation of the Survival for Interval Censored Data". Statistics in Medicine, 19, 2611-2624. (Also Report 1997-014, Division of Biostatistics, University of Minnesota, 1997)
  4. Pan, W. (2000) ``A Multiple Imputation Approach to Cox Regression with Interval Censored Data". Biometrics, 56, 192-203. (Also Report 1999-010, Division of Biostatistics, University of Minnesota, 1999)
  5. Pan, W. (2000) ``A Two-Sample Test with Interval Censored Data via Multiple Imputation". Statistics in Medicine, 19, 1-11. (Also Report 1999-003, Division of Biostatistics, University of Minnesota, 1999)
  6. Pan, W. and Chappell, R. (1999) ``A Note on Inconsistency of NPMLE of the Distribution Function from Left-truncated and Interval-censored Data". Lifetime Data Analysis, 5, 281-291. (Also Report 1998-003, Division of Biostatistics, University of Minnesota, 1998)
  7. Pan, W. (1999) ``A Comparison of Some Two-Sample Tests with Interval Censored Data". Journal of Nonparametric Statistics, 12, 133-146.
  8. Pan, W. (1999) ``Extending the Iterative Convex Minorant Algorithm to the Cox Model for Interval Censored Data". Journal of Computational and Graphical Statistics, 8, 191-200. (Also Report 1997-013, Division of Biostatistics, University of Minnesota, 1997)
  9. Pan, W. (1998) ``Rank Invariant Tests with Left Truncated and Interval Censored Data". Journal of Statistical Computation and Simulation, 61, 163-174.
  10. Pan, W. and Chappell, R. (1998) ``A Nonparametric Estimator of Survival Functions for Arbitrarily Truncated and Censored Data". Lifetime Data Analysis, 4, 187-202.
  11. Pan, W. and Chappell, R. (1998) ``Computation of the NPMLE of Distribution Functions for Interval Censored and Truncated Data with Applications to the Cox Model". Computational Statistics and Data Analysis, 28, 33-50.
  12. Pan, W. and Chappell, R. (1998) ``Estimating Survival Curves with Left-truncated and Interval-censored Data via the EMS Algorithm". Communications in Statistics -- Theory and Methods, 27, 777-793.
  13. Pan, W., Chappell, R. and Kosorok, M.R. (1998) ``On Consistency of the Monotone MLE of Survival for Left Truncated and Interval Censored Data". Statistics and Probability Letters, 38, 49-57.
  14. Pan, W. and Chappell, R. (1998) ``Estimating Survival Curves with Left-truncated and Interval-censored Data Under Monotone Hazards". Biometrics, 54, 1053-1060.

Multivariate survival analysis with right censored data

  1. Pan, W. (2001) ``Using Frailties in the Accelerated Failure Time Model". Lifetime Data Analysis, 7, 55-64. (Also Report 2000-027, Division of Biostatistics, University of Minnesota, 2000)
  2. Pan, W. and Connett, J.E. (2001) ``A Multiple Imputation Approach to Linear Regression with Clustered Censored Data". Lifetime Data Analysis, 7, 111-123. (Also Report 2000-025, Division of Biostatistics, University of Minnesota, 2000)
  3. Pan, W. and Louis, T.A. (2000) ``A Linear Mixed-Effects Model for Multivariate Censored Data". Biometrics, 56, 160-166. (Also Report 1998-019, Division of Biostatistics, University of Minnesota, 1998)
  4. Pan, W. and Kooperberg, C. (1999) ``Linear Regression for Bivariate Censored Data via Multiple Imputation". Statistics in Medicine, 18, 3111-3121. (Also Report 1999-002, Division of Biostatistics, University of Minnesota, 1999)

Pattern recognition, computing and others

  1. Pan, W. (2001) ``Approximate Confidence Intervals for One Proportion and Difference of Two Proportions". Computational Statistics and Data Analysis, 40, 143-157. (Also Report 2001-026, Division of Biostatistics, University of Minnesota, 2001)
  2. Pan, W. (1999) ``Shrinking Classification Trees for Bootstrap Aggregation". Pattern Recognition Letters, 20, 961-965. (Also Report 1998-006, Division of Biostatistics, University of Minnesota, 1998)
  3. Pan, W. (1999) ``Bootstrapping Likelihood for Model Selection with Small Samples". Journal of Computational and Graphical Statistics, 8, 687-698. (Also Report 1998-005, Division of Biostatistics, University of Minnesota, 1998)
  4. Pan, W. and Louis, T.A. (1999) ``Two Semi-parametric Empirical Bayes Estimators". Computational Statistics and Data Analysis, 30, 185-196. (Also Report 1998-020, Division of Biostatistics, University of Minnesota, 1998)
  5. Pan, W. (1998) ``Bias/Variance Tradeoff in Combining Subsample Estimates for a Very Large Data Set". Computing Science and Statistics, 30, 379-381. (Also Report 1998-025, Division of Biostatistics, University of Minnesota, 1998)
  6. Pan, W. (1998) ``Bagging Empirical Bayes Estimators". Proceedings of the Section on Bayesian Statistical Science of the American Statistical Association, 28-31.
  7. Pan, W., Li, L. and Zhang, X. (1991) ``Words Segmentation in Chinese Hand written Documents". Proc. of the Chinese National Conference on Artificial Intelligence and Pattern Recognition. 300-303, Harbin, China.
  8. Li, L., Pan, W. and Zhang, X. (1991) ``An Algorithm of Segmenting Characters in Scripted Documents". Proc. of the Chinese National Conference on Artificial Intelligence and Pattern Recognition. 304-307, Harbin, China.
  9. Pan, W., Jiang, X., Li, L. and Zhang, X. (1991) ``KxK Thinning". Proc. of the Second Chinese National Conference on Computer Vision and Intelligent Control. 248-252, Wuhan, China.
  10. Pan, W., Jiang, X., Zhang, X. (1990) ``Preprocessing of Handwritten Chinese Character Recognition". Proc. of Computer Science Graduates Conference, Chinese Academy of Sciences, Beijing, China.