Papers by Subject Area
Gene expression data analysis
- Pan, W. (in press).
``Incorporating Gene Functional Annotations in
Detecting Differential Gene Expression".
To appear Applied Statistics.
- 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)
- 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)
- 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)
- 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)
- 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)
- 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.
- 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)
- 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)
- 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)
- 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)
- 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)
- 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)
- 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.
- 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)
- 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)
- 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)
- 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.
- 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.
- 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)
-
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)
- 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)
-
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
- 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)
- 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.
- 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)
- 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)
- 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)
- 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)
-
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)
-
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)
-
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)
-
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)
-
Pan, W. (2001)
``Model Selection in Estimating Equations".
Biometrics, 57, 529-534.
(Also Report
2000-028, Division of Biostatistics,
University of Minnesota, 2000)
-
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)
-
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)
-
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
-
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)
-
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)
-
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)
-
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)
-
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)
-
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)
-
Pan, W. (1999) ``A Comparison of Some Two-Sample Tests with
Interval Censored Data".
Journal of Nonparametric Statistics, 12, 133-146.
-
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)
-
Pan, W. (1998)
``Rank Invariant Tests with Left Truncated and Interval Censored Data".
Journal of Statistical Computation and Simulation, 61, 163-174.
-
Pan, W. and Chappell, R. (1998)
``A Nonparametric Estimator of Survival Functions
for Arbitrarily Truncated and Censored Data".
Lifetime Data Analysis, 4, 187-202.
-
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.
-
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.
-
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.
-
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
-
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)
-
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)
-
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)
-
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
-
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)
-
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)
-
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)
-
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)
- 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)
- Pan, W. (1998) ``Bagging Empirical Bayes Estimators".
Proceedings of the Section on Bayesian Statistical Science of
the American Statistical Association, 28-31.
-
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.
-
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.
-
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.
-
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.