A few relevant Duke papers

• Gene Pathway Applications using Factor Regression Models

  • (paper) Erich Huang, Seiichi Ishida, Jennifer Pittman, Holly Dressman, Andrea Bild, Mark D'Amico, Richard Pestell, Mike West and Joseph R Nevins, Gene expression phenotypic models that predict the activity of oncogenic pathways, 2003, Nature Genetics, 34,226-130 .
    
  • (paper) E.P. Black, E. Huang, H. Dressman, S. Ishida, M. West and J.R. Nevins (2003) Distinct gene expression phenotypes of cells lacking Rb and Rb family members. Cancer Genetics, 63, 3716-3723.
    
  • (paper) R. Spang, H. Zuzan, M. West, J.R. Nevins, J.R. Marks & C. Blanchette (2001) Prediction and uncertainty in the analysis of gene expression profiles In Silico Biology.
    
  • S. Ishida, E. Huang, H. Zuzan, R. Spang, G. Leone, M. West and J.R. Nevins (2001) Role for E2F in control of both DNA replication and mitotic functions as revealed from DNA microarray analysis. Molecular and Cellular Biology, 21, 4684-99.

• Graphical Models
  
  
  • (paper) Adrian Dobra, Beatrix Jones, Chris Hans, Joseph R. Nevins and Mike West, Sparse graphical models for exploring gene expression data, 2004, J. Mult. Analysis (in press).
    
  • (paper) Beatrix Jones, Adrian Dobra, Carlos Carvalho, Chris Hans, Chris Carter and Mike West, Experiments in stochastic computation for high-dimensional graphical models, 2004, (submitted).

• Expression Array Issues, Basics
  
  
  • (paper) E.P. Hoffman, T. Awad, A. Spira, J. Palma, T. Webster , G. Wright, J. Buckley, R. Davis, E. Hubbell, W. Jones, R. Tibshirani, R. Tompkins, T. Triche, W. Xiao, M. West and J.A. Warrington. Expression profiling: Best practices for Affymetrix array data generation and interpretation for clinical trials, 2004, Nature Reviews Genetics , 4, 229-237.

• Prediction Tree Models and Genomic/Clinico-Genomic Applications
  
  
  • (paper) Jennifer Pittman, Erich Huang, Joseph Nevins and Mike West, Prediction tree models in clinico-genomics, 2003, Bulletin of the International Statistical Institute, ISI 54th Session, 76.
    
  • (paper) Jennifer Pittman, Erich Huang, Quanli Wang, Joseph R Nevins and Mike West, Bayesian analysis of binary prediction tree models for retrospectively sampled outcomes, 2004, Biostatistics (in press).
    
  • (abstract) Jennifer Pittman, Erich Huang, Holly Dressman, Cheng-Fang Horng, Skye H Cheng, Mei-Hua Tsou, Chii-Ming Chen, Andrea Bild, Edwin S Iversen, Ming Liao, Andrew T Huang, Joseph R Nevins and Mike West, Integrated modelling of clinical and gene expression information for personalized prediction of disease outcomes, 2004, PNAS, 101, 8431-8436
    
  • (paper) Joe Nevins, Erich Huang, Holly Dressman, Jennifer Pittman, Andrew Huang and Mike West, Towards integrated clinico-genomic models for personalized medicine: Combining gene expression signatures and clinical factors in breast cancer outcomes prediction, 2003, Human Molecular Genetics, 12, 153-157.
    
  • (paper) Erich Huang, Skye H Cheng, Holly Dressman, Jennifer Pittman, Mei-Hua Tsou, Cheng-Fang Horng, Andrea Bild, Edwin S Iversen, Ming Liao, Chii-Ming Chen, Mike West, Joseph R Nevins and Andrew T Huang,
    Gene expression predictors of breast cancer outcomes, 2004, Lancet, 361, 1590-1596.
    
  • (paper) Erich Huang, Mike West and Joseph R Nevins, Gene expression profiles and predicting clinical characteristics of breast cancer, 2003, Hormone Res., 58, 55-73.

• Factor Regression Models and Gene Expression Phenotyping
  • (paper) M. West (2003) Bayesian factor regression models in the "Large p, Small n" paradigm Bayesian Statistics, 7, 723-732.
    
  • (paper) M. West, C. Blanchette, H. Dressman, E. Huang, S. Ishida, R. Spang, H. Zuzan, J.R. Marks and J. R. Nevins (2001) Predicting the clinical status of human breast cancer using gene expression profiles Proceedings of the National Academy of Sciences, 98, 11462-11467.
    
  • (paper) M. West, J.R. Nevins, J.R. Marks, C. Blanchette, R. Spang & H. Zuzan (2000) DNA microarray data analysis and regression modeling for genetic expression profiling