W Pan

Summary

Affiliation: University of Minnesota
Country: USA

Publications

  1. pmc Functional group-based linkage analysis of gene expression trait loci
    Na Li
    Division of Biostatistics, University of Minnesota, A460 Mayo Building MMC 303, 420 Delaware Street Southeast, Minneapolis, Minnesota 55126, USA
    BMC Proc 1:S117. 2007
  2. pmc Genome-wide localization of mobile elements: experimental, statistical and biological considerations
    Betsy M Martinez-Vaz
    Department of Biochemistry, Molecular Biology and Biophysics and BioTechnology Institute, University of Minnesota, Saint Paul, MN 55108, USA
    BMC Genomics 6:81. 2005
  3. pmc Operon information improves gene expression estimation for cDNA microarrays
    Guanghua Xiao
    Division of Biostatistics, School of Public Health, University of Minnesota, A460 Mayo Building, Minneapolis, MN 55455 0378, USA
    BMC Genomics 7:87. 2006
  4. pmc Network-based support vector machine for classification of microarray samples
    Yanni Zhu
    Division of Biostatistics, School of Public Health, University of Minnesota, Minneapolis, Minnesota 55455, USA
    BMC Bioinformatics 10:S21. 2009
  5. pmc A comparative study of discriminating human heart failure etiology using gene expression profiles
    Xiaohong Huang
    Division of Biostatistics, School of Public Health, University of Minnesota, Minneapolis, MN 55455, USA
    BMC Bioinformatics 6:205. 2005
  6. ncbi request reprint Incorporating gene functions as priors in model-based clustering of microarray gene expression data
    Wei Pan
    Division of Biostatistics, MMC 303, School of Public Health, University of Minnesota, Minneapolis, MN 55455 0392, USA
    Bioinformatics 22:795-801. 2006
  7. pmc Statistical tests of genetic association in the presence of gene-gene and gene-environment interactions
    Wei Pan
    Division of Biostatistics, School of Public Health, University of Minnesota, Minneapolis, Minn 55455 0392, USA
    Hum Hered 69:131-42. 2010
  8. pmc Adaptive tests for association analysis of rare variants
    Wei Pan
    Division of Biostatistics, School of Public Health, University of Minnesota, Minneapolis, MN 55455 0392, USA
    Genet Epidemiol 35:381-8. 2011
  9. ncbi request reprint A mixture model approach to detecting differentially expressed genes with microarray data
    Wei Pan
    Division of Biostatistics, School of Public Health, University of Minnesota, A460 Mayo, MMC 303, 420 Delaware Street SE, Minneapolis, MN 55455 0378, USA
    Funct Integr Genomics 3:117-24. 2003
  10. ncbi request reprint Semi-supervised learning via penalized mixture model with application to microarray sample classification
    Wei Pan
    Division of Biostatistics, School of Public Health, University of Minnesota, MN, USA
    Bioinformatics 22:2388-95. 2006

Collaborators

Detail Information

Publications92

  1. pmc Functional group-based linkage analysis of gene expression trait loci
    Na Li
    Division of Biostatistics, University of Minnesota, A460 Mayo Building MMC 303, 420 Delaware Street Southeast, Minneapolis, Minnesota 55126, USA
    BMC Proc 1:S117. 2007
    ..Future research is needed to develop rigorous methods in mapping of genes affecting the expression of a group of transcripts...
  2. pmc Genome-wide localization of mobile elements: experimental, statistical and biological considerations
    Betsy M Martinez-Vaz
    Department of Biochemistry, Molecular Biology and Biophysics and BioTechnology Institute, University of Minnesota, Saint Paul, MN 55108, USA
    BMC Genomics 6:81. 2005
    ....
  3. pmc Operon information improves gene expression estimation for cDNA microarrays
    Guanghua Xiao
    Division of Biostatistics, School of Public Health, University of Minnesota, A460 Mayo Building, Minneapolis, MN 55455 0378, USA
    BMC Genomics 7:87. 2006
    ..Therefore, techniques that can improve such estimations, and moreover are based on sound biological premises, are expected to benefit the field of microarray data analysis..
  4. pmc Network-based support vector machine for classification of microarray samples
    Yanni Zhu
    Division of Biostatistics, School of Public Health, University of Minnesota, Minneapolis, Minnesota 55455, USA
    BMC Bioinformatics 10:S21. 2009
    ..The main idea of this paper is to take full advantage of the biological observation that neighboring genes in a network tend to function together in biological processes and to embed this information into a formal statistical framework...
  5. pmc A comparative study of discriminating human heart failure etiology using gene expression profiles
    Xiaohong Huang
    Division of Biostatistics, School of Public Health, University of Minnesota, Minneapolis, MN 55455, USA
    BMC Bioinformatics 6:205. 2005
    ..In this paper we consider discriminating the etiologies of heart failure using gene expression libraries from two separate institutions...
  6. ncbi request reprint Incorporating gene functions as priors in model-based clustering of microarray gene expression data
    Wei Pan
    Division of Biostatistics, MMC 303, School of Public Health, University of Minnesota, Minneapolis, MN 55455 0392, USA
    Bioinformatics 22:795-801. 2006
    ..However, most existing methods, including model-based clustering, ignore known gene functions in clustering...
  7. pmc Statistical tests of genetic association in the presence of gene-gene and gene-environment interactions
    Wei Pan
    Division of Biostatistics, School of Public Health, University of Minnesota, Minneapolis, Minn 55455 0392, USA
    Hum Hered 69:131-42. 2010
    ..Unfortunately, Wang et al. did not include in their evaluations several powerful tests just recently discovered for analyzing multiple SNPs in a candidate gene or region...
  8. pmc Adaptive tests for association analysis of rare variants
    Wei Pan
    Division of Biostatistics, School of Public Health, University of Minnesota, Minneapolis, MN 55455 0392, USA
    Genet Epidemiol 35:381-8. 2011
    ..Our proposed tests are also general and flexible with the ability to incorporate weights on RVs and to adjust for covariates...
  9. ncbi request reprint A mixture model approach to detecting differentially expressed genes with microarray data
    Wei Pan
    Division of Biostatistics, School of Public Health, University of Minnesota, A460 Mayo, MMC 303, 420 Delaware Street SE, Minneapolis, MN 55455 0378, USA
    Funct Integr Genomics 3:117-24. 2003
    ..Several methods are proposed to effectively control the false positives. The methodology is applied to a data set containing expression levels of 1,176 genes of rats with and without pneumococcal middle ear infection...
  10. ncbi request reprint Semi-supervised learning via penalized mixture model with application to microarray sample classification
    Wei Pan
    Division of Biostatistics, School of Public Health, University of Minnesota, MN, USA
    Bioinformatics 22:2388-95. 2006
    ....
  11. ncbi request reprint Incorporating gene networks into statistical tests for genomic data via a spatially correlated mixture model
    Peng Wei
    Division of Biostatistics, School of Public Health, University of Minnesota, A460 Mayo Building MMC 303, Minneapolis, MN 55455 0378, USA
    Bioinformatics 24:404-11. 2008
    ..We applied the two approaches to a real ChIP-chip dataset (and simulated data) to identify the transcriptional target genes of TF GCN4. The new method was found to be more powerful in discovering the target genes...
  12. pmc Network-based model weighting to detect multiple loci influencing complex diseases
    Wei Pan
    Division of Biostatistics, MMC 303, School of Public Health, University of Minnesota, Minneapolis, MN 55455 0392, USA
    Hum Genet 124:225-34. 2008
    ....
  13. pmc Asymptotic tests of association with multiple SNPs in linkage disequilibrium
    Wei Pan
    Division of Biostatistics, School of Public Health, University of Minnesota, Minneapolis, Minnesota 55455 0392, USA
    Genet Epidemiol 33:497-507. 2009
    ..We recommend the routine use of two of the new tests, along with several other tests, to detect disease associations with multiple linked SNPs...
  14. pmc Network-based multiple locus linkage analysis of expression traits
    Wei Pan
    Division of Biostatistics, School of Public Health, University of Minnesota, Minneapolis, MN 55455 0378, USA
    Bioinformatics 25:1390-6. 2009
    ....
  15. pmc Incorporating predictor network in penalized regression with application to microarray data
    Wei Pan
    Division of Biostatistics, School of Public Health, University of Minnesota, Minneapolis, Minnesota 55455, USA
    Biometrics 66:474-84. 2010
    ....
  16. pmc A unified framework for detecting genetic association with multiple SNPs in a candidate gene or region: contrasting genotype scores and LD patterns between cases and controls
    Wei Pan
    Division of Biostatistics, MMC 303, School of Public Health, University of Minnesota, Minneapolis, MN 55455 0392, USA
    Hum Hered 69:1-13. 2010
    ....
  17. pmc Test selection with application to detecting disease association with multiple SNPs
    Wei Pan
    Division of Biostatistics, School of Public Health, University of Minnesota, Minneapolis, Minn 55455 0392, USA
    Hum Hered 69:120-30. 2010
    ....
  18. ncbi request reprint Small-sample adjustments in using the sandwich variance estimator in generalized estimating equations
    Wei Pan
    Division of Biostatistics, School of Public Health, University of Minnesota, Minneapolis, MN 55455 0378, USA
    Stat Med 21:1429-41. 2002
    ..In addition to hypothesis testing, our result has a clear implication on constructing Wald-type confidence intervals or regions...
  19. ncbi request reprint Sample size and power calculations with correlated binary data
    W Pan
    Division of Biostatistics, School of Public Health, University of Minnesota, Minneapolis, MN, USA
    Control Clin Trials 22:211-27. 2001
    ..The given formulas are based on using the robust variance estimator in GEE. We believe that these formulas will facilitate the practice in planning two-arm clinical trials with correlated binary outcome data...
  20. ncbi request reprint Linear regression for bivariate censored data via multiple imputation
    W Pan
    Division of Biostatistics, School of Public Health, University of Minnesota, A460 Mayo Building, Box 303, 420 Delaware Street SE, Minneapolis, MN 55455 0378, USA
    Stat Med 18:3111-21. 1999
    ..The methods are applied to a data set from an otitis media clinical trial...
  21. ncbi request reprint Estimating survival curves with left-truncated and interval-censored data under monotone hazards
    W Pan
    Division of Biostatistics, University of Minnesota, Minneapolis 55455 0378, USA
    Biometrics 54:1053-60. 1998
    ..The methodology is illustrated with the application to the Wisconsin Epidemiological Study of Diabetic Retinopathy data to estimate the probability of incidence of retinopathy...
  22. ncbi request reprint A two-sample test with interval censored data via multiple imputation
    W Pan
    Division of Biostatistics, School of Public Health, University of Minnesota, A460 Mayo Building Box 303, Minneapolis, MN 55455 0378, USA
    Stat Med 19:1-11. 2000
    ..The method is illustrated by reanalysing the Breast Cosmesis Study data set...
  23. ncbi request reprint A linear mixed-effects model for multivariate censored data
    W Pan
    Division of Biostatistics, School of Public Health, University of Minnesota, Minneapolis 55455 0378, USA
    Biometrics 56:160-6. 2000
    ..From simulation studies, this approach compares favorably with the marginal independence approach, especially when there is a strong within-cluster correlation...
  24. ncbi request reprint A multiple imputation approach to regression analysis for doubly censored data with application to AIDS studies
    W Pan
    Division of Biostatistics, School of Public Health, University of Minnesota, Minneapolis 55455 0378, USA
    Biometrics 57:1245-50. 2001
    ..Here we illustrate our method with an application to a formal goodness-of-fit test and a graphical check for the proportional hazards model for doubly censored data. We reanalyze a well-known AIDS data set...
  25. ncbi request reprint Smooth estimation of the survival function for interval censored data
    W Pan
    Division of Biostatistics, School of Public Health, University of Minnesota, A460 Mayo Building Box 303, Minneapolis, MN 55455 0378, USA
    Stat Med 19:2611-24. 2000
    ..The methods are illustrated by reanalysing the Breast Cosmesis Study data set...
  26. ncbi request reprint Graphical model checking with correlated response data
    W Pan
    Division of Biostatistics, School of Public Health, University of Minnesota, A460 Mayo Building, Box 303, 420 Delaware Street SE, Minneapolis, MN 55455 0378, USA
    Stat Med 20:2935-49. 2001
    ..The usefulness of the methodology is demonstrated through application to a correlated binary data set drawn from a clinical trial, the Lung Health Study...
  27. pmc How many replicates of arrays are required to detect gene expression changes in microarray experiments? A mixture model approach
    Wei Pan
    Division of Biostatistics, School of Public Health, University of Minnesota, 420 Delaware Street, Minneapolis, MN 55455 0378, USA
    Genome Biol 3:research0022. 2002
    ..Here, we discuss how to calculate the number of replicates in the context of applying a nonparametric statistical method, the normal mixture model approach, to detect changes in gene expression...
  28. ncbi request reprint Akaike's information criterion in generalized estimating equations
    W Pan
    Division of Biostatistics, University of Minnesota, Minneapolis 55455, USA
    Biometrics 57:120-5. 2001
    ..Its performance is investigated through simulation studies. For illustration, the method is applied to a real data set...
  29. ncbi request reprint Model selection in estimating equations
    W Pan
    Division of Biostatistics, University of Minnesota, Minneapolis 55455, USA
    Biometrics 57:529-34. 2001
    ..For illustration, the method is applied to a real data set taken from a study of the development of ewe embryos...
  30. ncbi request reprint A multiple imputation approach to Cox regression with interval-censored data
    W Pan
    University of Minnesota School of Public Health, Division of Biostatistics, Minneapolis 55455 0392, USA
    Biometrics 56:199-203. 2000
    ..Our proposal is easily implemented by taking advantage of existing computer programs for right-censored data...
  31. ncbi request reprint Using frailties in the accelerated failure time model
    W Pan
    Division of Biostatistics, School of Public Health, University of Minnesota, Minneapolis, MN, USA
    Lifetime Data Anal 7:55-64. 2001
    ..Through simulation it is shown that its performance compares favorably with that of the marginal independence approach. For illustration we reanalyze a real data set...
  32. ncbi request reprint Estimation in the cox proportional hazards model with left-truncated and interval-censored data
    Wei Pan
    Division of Biostatistics, School of Public Health, University of Minnesota, Minneapolis 55455, USA
    Biometrics 58:64-70. 2002
    ..Simulations were conducted to assess their performance. The methods are applied to the Massachusetts Health Care Panel Study data set to compare the probabilities of losing functional independence for male and female seniors...
  33. pmc Model-based cluster analysis of microarray gene-expression data
    Wei Pan
    Division of Biostatistics, School of Public Health, University of Minnesota, 420 Delaware Street SE, Minneapolis, MN 55455 0378, USA
    Genome Biol 3:RESEARCH0009. 2002
    ..Here, we introduce and illustrate its use in detecting differentially expressed genes. In particular, we do not cluster gene-expression patterns but a summary statistic, the t-statistic...
  34. ncbi request reprint A multiple imputation approach to linear regression with clustered censored data
    W Pan
    Division of Biostatistics, School of Public Health, A460 Mayo Building, University of Minnesota, Minneapolis, MN 55455, USA
    Lifetime Data Anal 7:111-23. 2001
    ..1993), which ignores the within-cluster correlation in estimating the regression coefficient. Our proposal is easy to implement by using existing softwares...
  35. ncbi request reprint A comparative review of statistical methods for discovering differentially expressed genes in replicated microarray experiments
    Wei Pan
    Division of Biostatistics, School of Public Health, University of Minnesota, A460 Mayo, MMC 303, 420 Delaware Street SE, Minneapolis, MN 55455 0378, USA
    Bioinformatics 18:546-54. 2002
    ..Genome Res., 11, 1227-1236, 2001) and a mixture model approach (Pan et al., http://www.biostat.umn.edu/cgi-bin/rrs?print+2001,2001a,b) with particular attention to their different modeling assumptions...
  36. ncbi request reprint Using weighted permutation scores to detect differential gene expression with microarray data
    Xu Guo
    Division of Biostatistics, School of Public Health, University of Minnesota, A460 Mayo Building, MMC 303, Minneapolis, MN 55455 0378, USA
    J Bioinform Comput Biol 3:989-1006. 2005
    ..Using simulated data and real data for time-course microarray experiments, we show the improved performance of the proposed methods when implemented in MMM, EB and SAM...
  37. ncbi request reprint A note on using permutation-based false discovery rate estimates to compare different analysis methods for microarray data
    Yang Xie
    Division of Biostatistics, School of Public Health, University of Minnesota Minneapolis, MN 55455, USA
    Bioinformatics 21:4280-8. 2005
    ..Second, we propose a simple modification of the standard permutation to yield a better FDR estimator, which can in turn serve as a more fair criterion to evaluate various statistical methods...
  38. ncbi request reprint Machine safety evaluation in small metal working facilities: an evaluation of inter-rater reliability in the quantification of machine-related hazards
    Kaizad Munshi
    Park Nicollet Institute, Minneapolis, Minnesota, USA
    Am J Ind Med 48:381-8. 2005
    ..The study reported here involved the development and evaluation of methods for measuring machine safety, which will be used in the intervention study...
  39. pmc A Bayesian approach to joint modeling of protein-DNA binding, gene expression and sequence data
    Yang Xie
    Division of Biostatistics, Department of Clinical Sciences, University of Texas Southwestern Medical Center at Dallas, Dallas, TX, USA
    Stat Med 29:489-503. 2010
    ....
  40. ncbi request reprint Statistical significance analysis of longitudinal gene expression data
    Xu Guo
    Division of Biostatistics, School of Public Health, University of Minnesota, A460 Mayo Building, MMC 303, Minneapolis, MN 55455 0378, USA
    Bioinformatics 19:1628-35. 2003
    ..It is well known in other applications that valid statistical analyses have to appropriately take account of the possible within-subject correlation in longitudinal data...
  41. ncbi request reprint Linear regression and two-class classification with gene expression data
    Xiaohong Huang
    Division of Biostatistics, School of Public Health, University of Minnesota, A460 Mayo Building MMC 303, Minneapolis, MN 55455 0378, USA
    Bioinformatics 19:2072-8. 2003
    ..the compound covariate method of Hedenfalk et al. (originally proposed by Tukey), and the shrunken centroids method of Tibshirani et al. These methods look different and are more or less ad hoc...
  42. ncbi request reprint Combining gene annotations and gene expression data in model-based clustering: weighted method
    Desheng Huang
    Division of Biostatistics, School of Public Health, University of Minnesota, Minneapolis, 55455, USA
    OMICS 10:28-39. 2006
    ..We use simulated data and real data to demonstrate the feasibility and advantages of the proposed method...
  43. ncbi request reprint Incorporating prior knowledge of predictors into penalized classifiers with multiple penalty terms
    Feng Tai
    Division of Biostatistics, School of Public Health, University of Minnesota, A460 Mayo Building MMC 303, Minneapolis, MN 55455 0378, USA
    Bioinformatics 23:1775-82. 2007
    ....
  44. ncbi request reprint Modified nonparametric approaches to detecting differentially expressed genes in replicated microarray experiments
    Yanli Zhao
    Division of Biostatistics, School of Public Health, University of Minnesota, MMC 303, A460 Mayo Building, 420 Delaware Street SE, Minneapolis, MN 55455, USA
    Bioinformatics 19:1046-54. 2003
    ..However, relatively little effort has been directed toward assessment of the performance or the underlying assumptions of the methods in constructing such test and null statistics...
  45. ncbi request reprint Incorporating prior information via shrinkage: a combined analysis of genome-wide location data and gene expression data
    Yang Xie
    Division of Biostatistics, School of Public Health, University of Minnesota, Minneapolis, MN, USA
    Stat Med 26:2258-75. 2007
    ..This method can also be used to incorporate other information, such as gene ontology (GO), to microarray data analysis to detect differentially expressed genes...
  46. ncbi request reprint Incorporating prior knowledge of gene functional groups into regularized discriminant analysis of microarray data
    Feng Tai
    Division of Biostatistics, School of Public Health, University of Minnesota, A460 Mayo Building MMC 303, Minneapolis, MN 55455 0378, USA
    Bioinformatics 23:3170-7. 2007
    ..We show that one of the proposed methods performed better than PAM and SCRDA in a simulation study and several real data examples...
  47. ncbi request reprint On the use of permutation in and the performance of a class of nonparametric methods to detect differential gene expression
    Wei Pan
    Division of Biostatistics, School of Public Health, University of Minnesota, A460 Mayo Building MMC 303, Minneapolis, MN 55455 0378, USA
    Bioinformatics 19:1333-40. 2003
    ..This observation may apply to other permutation-based nonparametric methods. We propose a new method of constructing a null statistic that aims to estimate the null distribution of a test statistic directly...
  48. ncbi request reprint Modeling the relationship between LVAD support time and gene expression changes in the human heart by penalized partial least squares
    Xiaohong Huang
    Division of Biostatistics, School of Public Health, University of Minnesota, A460 Mayo Building, MMC 303, Minneapolis, MN 55455 0378, USA
    Bioinformatics 20:888-94. 2004
    ..The heart failure patients in our study were supported by the LVAD for various periods of time. The goal of this study is to model the relationship between the time of LVAD support and gene expression changes...
  49. doi request reprint Incorporating gene functions into regression analysis of DNA-protein binding data and gene expression data to construct transcriptional networks
    Peng Wei
    Division of Biostatistics, School of Public Health, University of Minnesota, A460 Mayo Building, MMC 303, Minneapolis, MN 55455 0378, USA
    IEEE/ACM Trans Comput Biol Bioinform 5:401-15. 2008
    ..In particular, we find that the shrinkage method consistently works well under various scenarios. We recommend the use of the shrinkage method as a useful alternative to the existing methods...
  50. ncbi request reprint Mapping safety interventions in metalworking shops
    Lisa M Brosseau
    Division of Environmental Health Sciences, University of Minnesota, School of Public Health, Minneapolis, MN 55455, USA
    J Occup Environ Med 49:338-45. 2007
    ..This paper describes the selection of intervention activities designed to lower machine-related hazards and amputations in small metal fabrication businesses...
  51. pmc Effectiveness of a worksite intervention to reduce an occupational exposure: the Minnesota wood dust study
    DeAnn Lazovich
    Division of Epidemiology, University of Minnesota, Minneapolis, Minneapolis, MN 55454, USA
    Am J Public Health 92:1498-505. 2002
    ..This study assessed the effectiveness of an intervention to reduce wood dust, a carcinogen, by approximately 26% in small woodworking businesses...
  52. ncbi request reprint Analysis by cDNA microarrays of altered gene expression in middle ears of rats following pneumococcal infection
    Jizhen Lin
    Department of Otolaryngology, University of Minnesota Otitis Media Research Center, University of Minnesota School of Medicine, 2001 Sixth Street S E, Room 216, Minneapolis, MN 55455, USA
    Int J Pediatr Otorhinolaryngol 65:203-11. 2002
    ..The purpose of this study is to explore the cellular and molecular basis that remains on a longer time after acute pneucmococcal middle ear infection and potentiates development of thick effusion in the middle ear...
  53. ncbi request reprint A comparison of the perceptions and beliefs of workers and owners with regard to workplace safety in small metal fabrication businesses
    David Parker
    Park Nicollet Institute, Minneapolis, Minnesota 55426, USA
    Am J Ind Med 50:999-1009. 2007
    ..Problems of improving safety in small business establishments may include a lack of resources, limited unionization, and an informal management structure...
  54. pmc The Research Diagnostic Criteria for Temporomandibular Disorders. V: methods used to establish and validate revised Axis I diagnostic algorithms
    Eric L Schiffman
    Department of Diagnostic and Biological Sciences, University of Minnesota, Minneapolis, MN 55455, USA
    J Orofac Pain 24:63-78. 2010
    ..Cutoff points for target validity were sensitivity > or = 0.70 and specificity > or = 0.95. Reliability of revised algorithms was assessed in 27 study participants...
  55. pmc A randomized, controlled intervention of machine guarding and related safety programs in small metal-fabrication businesses
    David L Parker
    Park Nicollet Institute, Minneapolis, MN, USA
    Public Health Rep 124:90-100. 2009
    ..The absence of machine guarding and related programs such as lockout/tagout may result in serious injury or death. The purpose of this study was to improve machine-related safety in small metal-fabrication businesses...
  56. ncbi request reprint Variable selection in penalized model-based clustering via regularization on grouped parameters
    Benhuai Xie
    Division of Biostatistics, School of Public Health, University of Minnesota, Minneapolis, Minnesota 55455, USA
    Biometrics 64:921-30. 2008
    ..Simulation studies and applications to microarray gene expression data for cancer subtype discovery demonstrate the advantage of the new proposal over several existing approaches...
  57. ncbi request reprint Identification of gene expression profiles in rat ears with cDNA microarrays
    Jizhen Lin
    Department of Otolaryngology, University of Minnesota Medical School, Division of Biostatistics, Minneapolis, MN 55455, USA
    Hear Res 175:2-13. 2003
    ....
  58. ncbi request reprint Gene function prediction by a combined analysis of gene expression data and protein-protein interaction data
    Guanghua Xiao
    Division of Biostatistics, School of Public Health, University of Minnesota, A460 Mayo Building MMC 303, Minneapolis, MN 55455 0378, USA
    J Bioinform Comput Biol 3:1371-89. 2005
    ..Finally, we propose a logistic regression method that is flexible enough to combine information from any number of data sources while maintaining computational feasibility...
  59. pmc A data-adaptive sum test for disease association with multiple common or rare variants
    Fang Han
    Division of Biostatistics, School of Public Health, University of Minnesota, Minneapolis, MN 55455 0392, USA
    Hum Hered 70:42-54. 2010
    ..We show that the proposed test has high power across a wide range of scenarios with either common or rare variants, or both. In particular, in some situations the proposed test performs better than several commonly used methods...
  60. pmc Penalized mixtures of factor analyzers with application to clustering high-dimensional microarray data
    Benhuai Xie
    Division of Biostatistics, School of Public Health and School of Statistics, University of Minnesota, Minneapolis, MN, USA
    Bioinformatics 26:501-8. 2010
    ..We use simulated data and real microarray data to illustrate the utility and advantages of the proposed method over several existing ones...
  61. pmc Binomial mixture model-based association tests under genetic heterogeneity
    Hui Zhou
    Division of Biostatistics, University of Minnesota, Minneapolis, MN 55455, USA
    Ann Hum Genet 73:614-30. 2009
    ..We show with a wide spectrum of numerical examples that under genetic heterogeneity the proposed tests are more powerful than some commonly used association tests...
  62. ncbi request reprint Comparing three methods for variance estimation with duplicated high density oligonucleotide arrays
    Xiaohong Huang
    Division of Biostatistics, School of Public Health, University of Minnesota, A460 Mayo Building MMC 303, Minneapolis 55455 0378, USA
    Funct Integr Genomics 2:126-33. 2002
    ..Our results indicate that the three methods give variance estimates close to each other. Due to its simplicity and generality, we recommend the use of the smoothed sample variance for data with a small number of replicates...
  63. ncbi request reprint Borrowing information from relevant microarray studies for sample classification using weighted partial least squares
    Xiaohong Huang
    Division of Biostatistics, School of Public Health, University of Minnesota, A460 Mayo Building MMC 303, Minneapolis, MN 55455 0378, USA
    Comput Biol Chem 29:204-11. 2005
    ..Second, WPLS/WPPLS performs better than the standard approach of combining multiple classifiers. Third, WPPLS can improve over WPLS, just as PPLS does over PLS for a single dataset...
  64. pmc Identification of genes responsible for osteoblast differentiation from human mesodermal progenitor cells
    Huilin Qi
    Stem Cell Institute, Division of Hematology, Oncology, and Transplantation, Department of Medicine, University of Minnesota Medical School, Minneapolis, MN 55445, USA
    Proc Natl Acad Sci U S A 100:3305-10. 2003
    ..These studies indicate that in vitro differentiation cultures in which MPCs are induced to one of multiple cell fates should be very useful for defining signals important for lineage-specific differentiation...
  65. ncbi request reprint Profile of machine safety in small metal fabrication businesses
    Yogindra Samant
    Park Nicollet Institute, Minneapolis, Minnesota, USA
    Am J Ind Med 49:352-9. 2006
    ..Metal working has been identified as an industry with one of the highest rates of non-fatal injury in the United States. However, the systematic evaluation of machine-related hazards is lacking...
  66. pmc Differential endothelial cell gene expression by African Americans versus Caucasian Americans: a possible contribution to health disparity in vascular disease and cancer
    P Wei
    Vascular Biology Center, Department of Medicine, Medical School, University of Minnesota, Minneapolis, MN 55455, USA
    BMC Med 9:2. 2011
    ....
  67. ncbi request reprint Small-sample performance of the robust score test and its modifications in generalized estimating equations
    Xu Guo
    Division of Biostatistics, School of Public Health, University of Minnesota, Minneapolis, MN 55455, USA
    Stat Med 24:3479-95. 2005
    ..Finally, we demonstrate the utility of our proposal by applying it to a group-randomized clinical trial, trying alternative cafeteria options in schools (TACOS)...
  68. ncbi request reprint A practical question based on cross-platform microarray data normalization: are BOEC more like large vessel or microvascular endothelial cells or neither of them?
    Aixiang Jiang
    Division of Cancer Biostatistics, Department of Biostatistics, Vanderbilt University, Nashville, TN 37232, USA
    J Bioinform Comput Biol 5:875-93. 2007
    ..Based on all the common genes between the two platforms, SVM analysis further confirmed this conclusion...
  69. ncbi request reprint Organizational characteristics of small metal-fabricating businesses in Minnesota
    Yogindra Samant
    Norwegian Authority of Labor Inspection, Trondheim, Norway
    Int J Occup Environ Health 13:160-6. 2007
    ..Financial capability had no bearing on ability of a small business to mount an OHS programs. Non-unionized small businesses may be more vulnerable to occupational injuries...
  70. ncbi request reprint Does it always help to adjust for misclassification of a binary outcome in logistic regression?
    Xianqun Luan
    Division of Biostatistics and Epidemiology, The Children s Hospital of Philadelphia, 3535 Market St, 14th Floor, Philadelphia, PA 19104, USA
    Stat Med 24:2221-34. 2005
    ..In the context of a data set on agricultural injuries, numerical evidence is provided through simulation studies...
  71. ncbi request reprint An examination of the process of relapse prevention therapy designed to aid smoking cessation
    Bertram Stöffelmayr
    Department of Psychiatry, Michigan State University, East Lansing, MI 48824, USA
    Addict Behav 28:1351-8. 2003
    ....
  72. doi request reprint Alternate arrangement of PpL B3 domain and SpA D domain creates synergistic double-site binding to VH3 and Vkappa regions of fab
    Shaohua H Jiang
    Department of Microbiology, Second Military Medical University, Shanghai, China
    DNA Cell Biol 27:423-31. 2008
    ..The demonstration of this novel binding property would promote to achieve the designed hybrid IBPs for useful immunological applications...
  73. ncbi request reprint Persistence of the effect of the Lung Health Study (LHS) smoking intervention over eleven years
    Robert P Murray
    Department of Community Health Sciences, University of Manitoba, Winnipeg, MB, Canada R3A 1R9
    Prev Med 35:314-9. 2002
    ..This paper examined the quitting behavior of individuals who were randomized to a smoking cessation intervention (SI) or to usual care (UC), at a point approximately 11 years later...
  74. ncbi request reprint Incorporating biological knowledge into distance-based clustering analysis of microarray gene expression data
    Desheng Huang
    Department of Mathematics, China Medical University Shenyang, China
    Bioinformatics 22:1259-68. 2006
    ..A simulation study and an application to gene function prediction for the yeast demonstrate the advantage of our proposal over the standard method...
  75. ncbi request reprint [Differential expression of mitochondrial proteins in hepatoma cells analyzed using two-dimensional electrophoresis]
    Xing Li
    Department of Medical Laboratory, Chongqing University of Medical Sciences, Chongqing, 400016, PR China
    Ai Zheng 24:1327-31. 2005
    ..This study was to identify the differentially expressed mitochondrial proteins in hepatoma cells using two-dimensional gel electrophoresis (2-DE)...
  76. ncbi request reprint [Serum levels of IFN-gamma and IL-4 in children with Mycoplasmal pneumonia at the acute phase]
    Wei Pan
    Department of Pediatrics, Second Clinical Hospital, Jilin University, Changchun 130041, China
    Zhongguo Dang Dai Er Ke Za Zhi 8:373-5. 2006
    ..The aim of this study was to investigate the changes of IFN-gamma and IL-4 in peripheral blood of children with Mycoplasmal pneumonia...
  77. ncbi request reprint Immune responses against SARS-coronavirus nucleocapsid protein induced by DNA vaccine
    Ping Zhao
    Department of Microbiology, Second Military Medical University, 800 Xiangyin Road, Shanghai 200433, China
    Virology 331:128-35. 2005
    ..The results indicate that the N protein may be of potential value in vaccine development for specific prophylaxis and treatment against SARS...
  78. ncbi request reprint Statins are associated with a reduced incidence of perioperative mortality after coronary artery bypass graft surgery
    Wei Pan
    Division of Cardiovascular Anesthesiology, Texas Heart Institute, St Luke s Episcopal Hospital, Houston, Tex 77030, USA
    Circulation 110:II45-9. 2004
    ..We investigated the influence of preoperative statin therapy on adverse outcomes after primary coronary artery bypass graft (CABG) surgery...
  79. ncbi request reprint Myc-ARF (alternate reading frame) interaction inhibits the functions of Myc
    Abhishek Datta
    Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, 900 S Ashland Avenue, Chicago, IL 60607, USA
    J Biol Chem 279:36698-707. 2004
    ..Our results strongly suggest that cMyc is a bona fide target of ARF and that ARF attenuates c-Myc independently of the ARF-p53 axis...
  80. ncbi request reprint Inhibition of EGFP expression by siRNA in EGFP-stably expressing Huh-7 cells
    Mingmei Cao
    Department of Microbiology, Second Military Medical University, Shanghai 200433, China
    J Virol Methods 119:189-94. 2004
    ..This Huh-7-N/EGFP specific siRNA system has been proved reliable and convenient, and can also be applied widely as control in other RNA interference studies...
  81. ncbi request reprint Expression of human soluble gp190 in yeast Pichia pastoris
    Gang Li
    Department of Genetics and Eugenics, Chongqing Medical University, Chongqing 400016, China
    Yi Chuan Xue Bao 31:1182-9. 2004
    ..Biological activity assay showed that purified sgp190 could inhibit the effect of LIF on hCG biosynthesis of cytotrophoblast in vitro...
  82. ncbi request reprint Simultaneous confidence bounds for low-dose risk assessment with nonquantal data
    Walter W Piegorsch
    Department of Statistics, University of South Carolina, Columbia, South Carolina, USA
    J Biopharm Stat 15:17-31. 2005
    ..From the simultaneous confidence bounds, simultaneous lower limits on the benchmark dose associated with a particular risk are also constructed...
  83. ncbi request reprint Proactive telephone counseling as an adjunct to minimal intervention for smoking cessation: a meta-analysis
    Wei Pan
    Division of Educational Studies, University of Cincinnati, Cincinnati, OH 45221, USA
    Health Educ Res 21:416-27. 2006
    ..The results of this meta-analytic review imply that researchers and health care providers may need to focus on participants as much as on intervention process to obtain more effective interventions...
  84. ncbi request reprint Genistein stimulates the osteoblastic differentiation via NO/cGMP in bone marrow culture
    Wei Pan
    Institute of Clinical Pharmacology, Central South University, Changsha 410078, China
    J Cell Biochem 94:307-16. 2005
    ..Gen has estrogen-like activity and stimulates the proliferation and osteoblastic differentiation of mouse BMSCs at least in part through NO/cGMP pathway...
  85. ncbi request reprint 1,25-dihydroxyvitamin D3 suppresses renin gene transcription by blocking the activity of the cyclic AMP response element in the renin gene promoter
    Weihua Yuan
    Department of Medicine, Division of Biological Sciences, The University of Chicago, Chicago, Illinois 60637, USA
    J Biol Chem 282:29821-30. 2007
    ..These data indicate that 1,25(OH)(2)D(3) suppresses renin gene expression at least in part by blocking the formation of CRE-CREB-CBP complex...
  86. pmc Genetic endothelial systems biology of sickle stroke risk
    Liming Chang Milbauer
    Vascular Biology Center and Division of Hematology Oncology Transplantation, Department of Medicine, University of Minnesota Medical School, and Minneapolis Children s Hospital 55455, USA
    Blood 111:3872-9. 2008
    ....
  87. ncbi request reprint Family protection and prevention of alcohol use among Hispanic youth at high risk
    Elizabeth Sale
    Missouri Institute of Mental Health, 5400 Arsenal Street, St Louis, MO 63139, USA
    Am J Community Psychol 36:195-205. 2005
    ..Longitudinal growth curve analyses indicate that improving the connections that young Hispanic females have to their parents can have positive long-term effects on delaying or reducing their alcohol use...
  88. ncbi request reprint Analysis of reflection-peak wavelengths of sampled fiber Bragg gratings with large chirp
    Xihua Zou
    School of Information Science and Technology, Southwest Jiaotong University, Chengdu, 610031, China
    Appl Opt 47:4729-34. 2008
    ..Finally, the RPWs of SFBGs-LC can be achieved by combining the wavelength shift and the RPWs of equivalent U-SFBGs. Several simulations are shown to numerically confirm these predicted RPWs of SFBGs-LC...
  89. ncbi request reprint [Two-dimensional gel electrophoresis of subcellular fractions of hepatoma cells]
    Xing Li
    Department of Laboratory Sciences, Chongqing University of Medical Sciences, Chongqing 400016, China
    Zhonghua Gan Zang Bing Za Zhi 13:271-3. 2005
    ..To seek a better profiling of proteins of hepatoma cells...
  90. ncbi request reprint Small interfering RNA inhibits SARS-CoV nucleocapsid gene expression in cultured cells and mouse muscles
    Ping Zhao
    Department of Microbiology, Second Military Medical University, Shanghai, China
    FEBS Lett 579:2404-10. 2005
    ..Our findings suggest that the siRNA should provide the basis for prophylaxis and therapy of SARS-CoV infection in human...
  91. ncbi request reprint Small interfering RNA-mediated inhibition of hepatitis G virus gene expression in human hepatoma cell Huh-7
    Mingmei Cao
    Department of Microbiology, Second Military Medical University, Shanghai 200433, China
    Sci China C Life Sci 48:61-9. 2005
    ..In conclusion, the Huh-7-EH cells expressing HGV structural proteins stably can be used as a cell model for studying the replication of HGV and RNAi and the enlargement of RNAi may exist, in mammalian cells...
  92. ncbi request reprint ApoA-I structure on discs and spheres. Variable helix registry and conformational states
    Hui Hua Li
    Department of Pathology, The Wake Forest University Baptist Medical Center, Winston Salem, North Carolina 27157, USA
    J Biol Chem 277:39093-101. 2002
    ..Therefore, we conclude that as lipid-bound apoA-I adjusts from a discoidal to a spherical surface its intermolecular interactions are significantly reduced presumably to cover the increased surface area of the particle...

Research Grants8

  1. Model Building--Marginal Regression with Dependent Data
    Wei Pan; Fiscal Year: 2004
    ..All the techniques will be implemented in the commonly used statistical language S-Plus and made freely available to practitioners. ..
  2. Statistical Methods for Genomic and Proteomic Data
    Wei Pan; Fiscal Year: 2007
    ..We will extend PPLS to combine microarray data from multiple studies. We plan to implement the proposed statistical methods in R and make the software publicly and freely available. ..
  3. Statistical Methods for Genomic and Proteomic Data
    Wei Pan; Fiscal Year: 2009
    ....
  4. Statistical Methods for Genomic and Proteomic Data
    Wei Pan; Fiscal Year: 2010
    ....