FACULTY

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  Methodological Research

Survival Analysis

The Division is developing an international reputation as a locale for statistical research in the area of survival analysis and longitudinal data analysis. This area is anchored by the collaborative work of Mei-Jie Zhang, PhD with the researchers at Department of Biostatistics at the University of Copenhagen. Other faculty that have contributed to this area include: Brent Logan, PhD, Kwang Woo Ahn, PhD, Ruta Brazauskas, PhD, Rodney Sparapani, PhD, Soyoung Kim, PhD, and Noorie Hyun, PhD.

 

Clinical Trials

Brent Logan, PhD, working in the area of multiple comparisons, has interests in clinical trials with multiple end points and multiple decisions. He has proposed designs for randomized phase II clinical trials in which one is interested in evaluating several new treatments prior to a comparative phase III clinical trial. Professor Logan provides biostatistical support to a multicenter clinical trials network for blood and marrow transplant research.

 

Bayesian Methodology

Bayesian methodology is finding increasing number of applications in Biostatistics. This is reflected in the work of the faculty in the Division. Prakash Laud, PhD has been conducting methodological research in Bayesian nonparametric and semiparametric techniques, especially as applicable to survival data. He has also published papers in parametric Bayesian methodology, in linear and generalized linear models with an emphasis on model selection. Faculty members Brent Logan, PhD and Rodney Sparapani, PhD have been working on BART (Bayesian Additive Regression Trees) with applications to survival analysis and personalized medicine. Another faculty member, Anjishnu Banerjee, PhD, has been publishing papers on nonparametric methods. 

 

Multiple Comparisons

The problem of multiple comparisons arises when performing many hypothesis tests, in which case the “familywise error rate” or chance of one or more incorrect significant findings among all these tests increases with the number of tests being performed. Brent Logan, PhD has a keen interest in this area in which he continues to publish new methods and applications. Work with Daniel Rowe, PhD, has resulted in investigating multiple comparison thresholding techniques in single-subject fMRI analysis. Work with Ajit Tamhane, PhD, at Northwestern University includes the problem of comparing two treatments at multiple endpoints and multiple comparison procedures to identify the minimum effective dose and/or maximum safe dose in the dose-response setting. Collaboration with Mei-Jie Zhang, PhD, has investigated methods for controlling the familywise error rate when performing pairwise comparisons among several groups when the outcome is the time to an event of interest.

 

Statistical Genetics and Bioinformatics

The Division's research in statistical genetics is led by Tao Wang, PhD and Ying Liu, PhD, with recent work includes various genetic data analyses, linkage and association mapping of disease genes, modeling and methodology development for association mapping of quantitative trait loci, and haplotype association analysis of single nucleotide polymorphisms (SNPs). Specifically, Tao Wang, PhD, explored the definitions and properties of additive, dominance and epistatic effects of QTL and partition of genetic variance in an equilibrium as well as in a disequilibrium population. Additional work resulted in the development of a population-based multipoint LD method for fine mapping of quantitative trait loci. A mixture model was applied to describe the relationship between phenotype and QTL genotypes. An EM algorithm was developed to estimate the genetic effects of QTL and joint haplotype frequencies of QTL and markers. Ying Lui, PhD, is interested in developing methodology in statistical genetics, translational bioinformatics, microbiome, power and sample size calculation tool for NGS data, integrative/meta-analysis methods for different omics data, and supervised/unsupervised machine learning applications. For research interests in power and sample size calculation tool, he has focused on two applications in RNA-Seq and Methyl-Seq data. He has worked closely with collaborators from different fields, including cardiovascular epidemiology, psychiatry, and cancer biology. He has experiences in various types of omics data, including single nucleotide polymorphism (SNP), copy number variation (CNV), DNA methylation, gene expression, proteomics (peptide), and metabolomics data.

 

Variable Selection

Variable selection is one of the central issues in the application of statistical methods. Faculty members Kwang Woo Ahn, PhD and Soyoung Kim, PhD have been working on variable selection for survival and competing risks models with possibly high dimensional data.

 

Personalized Medicine

Personalized medicine has become an important research area in biostatistics. The main goal is developing a statistical tool to identify the optimal treatment given each patient’s characteristics. Faculty members Prakash Laud, PhD, Brent Logan, PhD, and Rodney Sparapani, PhD have been working on BART (Bayesian Additive Regression Trees) with applications to survival analysis and personalized medicine. Another faculty member, Ying Liu, PhD uses machine learning to develop new statistical techniques to find the optimal individualized treatment regime. Relatedly, Kwang Woo Ahn, PhD and Soyoung Kim, PhD have been working on this area using the propensity score for survival and competing risks outcomes.

  Publications/Presentations
  Collaborative Research

There are many research organizations within the College and its affiliates with whom the Division's faculty conduct joint research. Via Research Assistantships and Consulting Services students get an opportunity to work in collaborative projects with groups such as those below.

 

Biostatistics Consulting Service

The Medical College of Wisconsin Biostatistics Consulting Service provides statistical support to biomedical investigators.

 

BMTCTN

The Blood and Marrow Transplant Clinical Trials Network (BMTCTN) is a multi-center network funded by the NIH and NCI to implement clinical trials in the field of hematopoietic stem cell transplantation.

 

CIBMTR

The Center for International Blood and Marrow Transplant Research (CIBMTR) was formed ten years ago by a merger of the research efforts of the National Marrow Donor Program in Minneapolis and the International Blood and Marrow Transplant Registry (IBMTR) at the Medical College of Wisconsin.

 

Molecular Genetics

The Genomic Sciences and Precision Medicine Center at the Medical College of Wisconsin provides academic support for researchers at MCW who use the genomic sequence to understand disease and translate this information from the laboratory to the patient.

 

NMDP

The National Marrow Donor Program (NMDP) is the primary source of potential donors for patients seeking and unrelated hematopoietic stem cell transplantation.

 

PCOR

The Center for Patient Care and Outcomes Research (PCOR) at the Medical College of Wisconsin is made up of faculty and support staff who focus on research related to health care services and patient outcomes

  Technical Reports

Tech Report #66 August 2017 (PDF)
Evaluating Performance of Survival Regression Models with Interval Censored Data in Motor vehicle Crash Experiments
By: Anjishnu Banerjee, Narayan Yoganandan, Fang-Chi Hsu, Scott Gayzik, Frank Pintar

 

Tech Report #65 June 2017 (PDF)
Low Information Omnibus (LIO) Priors for Dirichlet Process Mixture Models
By: Yushu Shi, Michael Martens, Anjishnu Banerjee, Prakash Laud

 

Tech Report #64 April 2017 (PDF) data file (tar)
Nonparametric recurrent events analysis with BART and an application to the hospital admissions of patients with diabetes
By: Rodney Sparapani, Lisa Rein, Sergey Tarima, Tourette Jackson, John Meurer

 

Tech Report #63 March 2016 (PDF)
Accurately Approximating the log gamma distribution with a convolution of normals
By: Prakash Laud, Rodney Sparapani, Brent Logan

 

Tech Report #62 December 2014 (PDF)
Quantile residual lifetime analysis for dependent survival and competing risks data
By: kwang Woo Ahn, Brent Logan

Tech Report #61 December 2013 (PDF)
A proportional hazards regression model for the subdistribution with covariates adjusted censoring weight for competing risks data
By: Peng He, Tomas H. Scheike, Mei-Jie Zhang

 

Tech Report #60 December 2013 (PDF)
An approach for modeling cross-immunity of two strains, with application to variants of Bartonella in terms of genetic similarity
By: Kwang Woo Ahn, Michael Kosoy, Kung-Sik Chan

 

Tech Report #59 May 2013 (PDF)
Interim sample size recalculation for linear and logistic regression models: A comprehensive Monte-Carlo study
By: Sergey Tarima, Peng He, Tao Wang, Aniko Szabo

 

Tech Report #58 April 2012 (PDF)
Design Resampling for Interim Sample Size Recalculation
By: Sergey Tarima, Peng He, Tao Wang, Aniko Szabo

Tech Report #57 April 2012 (PDF)
Internal Pilot Studies: An Annotated Bibliography
By: Aniko Szabo, Tao Wang, Peng He, and Sergey Tarima

Tech Report #56 March 2012 (PDF)
Analysis of Paired and Clustered Time-to-Event Data: An Annotated Bibliography
By: Jennifer Le-Rademacher, John P. Klein, Ruta Brazauskas, and Aaron Katch

Tech Report #55 March 2008 (PDF)
Posterior Computation for Hierarchical Dirichlet Process Mixture Models: Application to Genetic Association Studies of Quantitative Traits in the Presence of Population Stratification
By: Nicholas M. Pajewski and Prakash Laud, PhD

 

  • STRUCTDPM.c (TXT): C code for implementing Bayesian Semiparametric modeling of Genetic Association Studies of Quantitative Traits in the Presence of Population Stratification.
  • STRUCTDPM_readme (PDF): is an instruction file for the program.

 

Tech Report #54 September 2005 (PDF)
Can we compute fMRI brain activation directly from k-space?
By: Daniel B. Rowe

Tech Report #53 December 2005 (PDF)
Multiple Treatments and Propensity Scores
By: Rodney Sparapani and Prakash Laud

Tech Report #52 July 2005 (PDF)
Models and Applications of Multivariate Statistical Analysis in fMRI
By: Daniel B. Rowe and Raymond G. Hofmann

Tech Report #51 July 2005 (PDF)
Correlated Noise of Fourier Reconstructed fMRI Data
By: Daniel B. Rowe and Raymond G. Hofmann

Tech Report #50 December 2004
A Non-Linear Model for Phase-Only fMRI data
By: Christopher P. Meller and Daniel B. Rowe

Tech Report #49 June 2004 (updated July 2010)
Some SAS macros for BUGS/WinBUGS data
By: Rodney Sparapani---More on SAS Macros

Tech Report #48 November 2004 (PDF)
A complex-valued fMRI data model for both magnitude and phase
By: Daniel B. Rowe

Tech Report #47 July 2004 (PDF)
A Complex fMRI Activation Model with a Temporally Varying Phase
By: Daniel B. Rowe and Brent R. Logan

Tech Report #46 May 2004 (PDF)
On Estimating the Parameters of the Complex fMRI Time Course Model
By Daniel B. Rowe

Tech Report #45 February 2004 (PDF)
An fMRI Activation Method Using Complex Data
By: Daniel B. Rowe and Brent R. Logan

Tech Report #44 2003 (PDF)
Additive hazards Markov regression models illustrated with bone marrow transplant data
By: Youyi Shu and John Klein

Tech Report #43 September 2003 (PDF)
Multiple Endpoints: An Overview and New Developments
By: Ajit C. Tamhane and Brent R. Logan

Tech Report #42 May 2003 (PDF)
The Effect of Correlation and Error Rate Specification On Thresholding Methods in fMRI Analysis
By: Brent R. Logan and Daniel B. Rowe

Tech Report #41 January 2003 (PDF)
fMRI Neurologic Synchrony Measures For Alzheimer's Patients With Monte Carlo Critical Values
By: Daniel B. Rowe

Tech Report #40 November 2002 (PDF)
Multivariate Regression Generalized Likelihood Ratio Tests for FMRI Activation
By: Daniel B. Rowe

Tech Report #39 June 2002 (PDF)
Computing FMRI Activations: Coefficients and t-Statistics by Detrending and Multiple Regression
By: Daniel B. Rowe and Steven W. Morgan

Tech Report #33 August 1999 (PDF)
A SAS Macro for the Positive Stable Frailty Model
By: Y. Shu and J. P. Klein

Tech Report #30 June 1998 (PDF)
Modeling Covariate Adjusted Mortality Relative to a Standard Population : Does Bone Marrow Transplantation Provide a Cure?
By: P. K. Andersen, M. M. Horowitz, J. P. Klein, G. Socie, J. Stone and M. J. Zhang

Tech Report #29 February 1998 (PDF)
Confidence Bands for the Difference of Two Survival Curves Under Proportional Hazards Model
By: M. J. Zhang and J. P. Klein

Tech Report #25 March 1997 (PDF)
Comparing Reference Charts for Cross-section and Longitudinal Data
By: T. H. Scheike, M. J. Zhang and A. Juul

Tech Report #24 February 1997 (PDF)
Grouped Failure Times, Tied Failure Times : Two Contributions to the Encyclopedia of Biostatistics
By: M. J. Zhang

Tech Report #23 January 1997 (PDF)
Testing for Center Effects in Multicenter Survival Studies: A Monte Carlo Comparison of Fixed and Random Effects Tests
By: P. K. Andersen, J. P. Klein and M. Zhang

Tech Report #22 December 1996 (PDF)
Survival Distributions and their Characteristics, a Contribution to the Encyclopedia of Biostatistics
By: J. P. Klein

Tech Report #21 December 1996 (PDF)
Determining when the Survival Rates of Two Treatments are the Same Based on a Censored Data Regression Model
By: J. P. Klein and M. Zhang

Tech Report #20 December 1996 (PDF)
Analysis of Variance with Structural Zeroes
By: T. H. Chelius and R. G. Hoffmann

Tech Report #19 September 1996 (PDF)
Modeling Multiple Nonlinear Time Series: A Graphical Approach to the Transfer Function
By: R. G. Hoffmann

Tech Report #18 September 1996 (PDF)
A SAS Macro for the Additive Hazards Regression Model
By: A. Howell and J. P. Klein

Tech Report #17 September 1996 (PDF)
Analysis of Survival Data : A Comparison of Three Major Statistical Packages (SAS, SPSS, BMDP)
By: C. J. Pelz and J. P. Klein

Tech Report #15 August 1996 (PDF)
Modeling Multistate Survival Illustrated in Bone Marrow Transplantation
By: J. P. Klein and C. Qian

Tech Report #13 July 1996 (PDF)
Confidence Regions for the Equality of Two Survival Curves
By: J. P. Klein and M. Zhang

Tech Report #12 January 1996 (PDF)
The Role of Frailty Models and Accelerated Failure Time Models in Describing Heterogeneity due to Omitted Covariates
By: N. Keiding, P. K. Andersen and J. P. Klein

Tech Report #10 September 1995 (PDF)
Estimation of Variance in Cox's Regression Model with Gamma Frailties
By: P. K. Andersen, J. P. Klein, K. M. Knudsen and R. T. y Palacios

Tech Report #9 July 1995 (PDF)
Predictive Specification of Prior Model Probabilities in Variable Selection
By: P. W. Laud and J. G. Ibrahim

Tech Report #6 November 1994 (PDF)
Predictive Model Selection
By: P. W. Laud and J. G. Ibrahim

Tech Report #5 August 1994 (PDF)
Sheppard's Correction for Grouping in Cox's Proportional Hazards Model
By: I. McKeague and M. Zhang

Tech Report #4 August 1994 (PDF)
Fitting Cox's Proportional Hazards Model Using Grouped Survival Data
By: I. McKeague and M. Zhang

Tech Report #3 August 1994 (PDF)
Statistical Challenges in Comparing Chemotherapy and Bone Marrow Transplantation as a Treatment for Leukemia
By: J. P. Klein and M. Zhang

Tech Report #2 December 1993 (PDF) -- (Table 5.1 (PDF)
Effects of Model Misspecification in Estimating Covariate Effects in Survival Analysis for Small Sample Sizes
By: Y. Li, J. P. Klein and M. L. Moeschberger

Tech Report #1 December 1993 (PDF)
Graphical Models for Panel Studies, Illustrated on Data from the Framingham Heart Study
By: J. P. Klein, N. Keiding and S. Kreiner