Publications by UVa Statistical Bioinformatics Group

  Peer-reviewed professional journals

          Gene Expression Data Analysis

  1. Tanabe L, Scherf U, Smith LH, Lee J.K., Hunter L, Weinstein JN  (1999). MedMiner: an Internet text-mining tool for biomedical information, with application to gene expression profiling. Biotechniques, 27(6):1210-4, 1216-7.
  2. Scherf, U., Ross, D.T., Waltham, M., Smith, L.H., Lee, J.K., Kohn, K.W., Reinhold, W.C., Myers, T.G., Andrews, D.T., Scudiero, D.A., Eisen, M.B., Sausville, E.A., Pommier, Y., Botstein, D., Brown, P.O., and Weinstein, J.N. (2000). A cDNA microarray gene expression database for the molecular pharmacology of cancer. Nature Genetics, 24 (3), 236-244.
  3. Shi, L.M., Fan, Y., Lee, J.K., Myers, T., Waltham, M., Andrews, A., Scherf, U., Paull, K., Weinstein, J.N. Mining and visualizing large anticancer drug databases. (2000). J. of Chem. Inf. & Com. Sci., 40 (2), 367-379.
  4. Weinstein, J.N., Waltham, M., Reinhold, W., Lee, J.K., Smith, L.H., Andrews, D., Tanabe, L., Zhou, Y., Myers, T.G., Buolamwini, J.K., and Scherf, U.  (2000) The current revolution in cancer drug discovery:  Genomics, proteomics, and bioinformatics.  Proc. Third Shizuoka Forum on Health and Longevity,   8 – 13.
  5. Woodfolk, J.A., Sung, S.J., Benjamin, D.C., Lee, J.K., Platts-Mills, T.A.E. (2000). Distinct human T cell repertoires mediate immediate and delayed-type hypersensitivity to the Trichophyton antigen, Tri r 21. J. of Immunology, 165, 4379-4387.
  6. Lee, J.K., Reinhold, W.O., Weinstein, J.N., Mesirov, J.P., Lander, E.S., Golub, T.R. (2001). Chemosensitivity prediction by transcriptional profiling. Proc Natl Acad Sci. 98:10787-92. 
  7. Lee, J.K.,  Scherf, U., Smith, LH, Tanabe, L., and Weinstein, J.N. (2001). Analysis of gene expression data of the NCI 60 cell lines using Bayesian hierarchical effects model, Proceedings of SPIE, BIOS 2001, Microarrays: Optical Technologies and Informatics, Vol. 2, 23, 228-235.
  8. Lee, J.K.(2001).  Analysis issues for gene expression array data, Clinical Chemistry 47, 1350-1352.
  9. Weinstein, J.N., Scherf, U., Lee, J.K., Nishizuka, S., Gwadry, F., Ajay, Bussey, K., Kim, S., Smith, L.H., Tanabe,L., Richman, S., Alexander, J., Kouros-Mehr, H., Maunakea, A., and Reinhold, W.C. (2002) The bioinformatics of Microarray gene expression profiling. Cytometry 47:46-49.
  10. Lankford, A.R., Byford, A.M., Ashton, K., French, B.A., Lee, J.K., Hedrick, J.P., Matherne, G.P. (2002) Gene expression profile of mouse myocardium with transgenic overexpression of A1 Adenosine Receptors, Physiological Genomics, 29, 11, 81-89. 
  11.  Lee, J.K(2002). Discovery and validation of microarray gene expression patterns, LabMedica International, 19, 2: 8-10.
  12. Jain, N ., Ley, K., Thatte, J., and Lee, J.K. (2003) Local pooled error test for identifying differentially expressed genes with a small number of replicated microarrays, Bioinformatics, 19 (15),  1945-51.           
  13. Nishizuka S, Chen ST, Gwadry FG, Alexander J, Major SM, Scherf U, Reinhold WC, Waltham M, Charboneau L, Young L, Bussey KJ, Kim S, Lababidi S, Lee J.K., Pittaluga S, Scudiero DA, Sausville EA, Munson PJ, Petricoin EF 3rd, Liotta LA, Hewitt SM, Raffeld M, Weinstein JN. (2003). Diagnostic markers that distinguish colon and ovarian adenocarcinomas: identification by genomic, proteomic, and tissue array profiling, Cancer Res. 63(17):5243-50.
  14. Kallmes DF, O E, Roy SS, Piccolo RG, Marx WF, Lee J.K., Jensen ME (2003). Radiation dose to the operator during vertebroplasty: prospective comparison of the use of 1-cc syringes versus an injection device, AJNR Am J Neuroradiol., 24(6):1257-60.
  15. Weinstein, J.N., Nishizuka, S., Reinhold, W.C., Bussey, K., Kim, S., Major, S., Lababidi, S., Feng, W., Wang, G., Raffeld, M., Sunshine, M., Narasimhan, S., Zeeberg, B., Wang, M., Lee, J.K., and Kane, D. Cancer drug discovery: Genomics, Proteomics, and Bioinformatics. Molecular Target Therapy of Cancer, Vol. 1, in press.
  16. Lee, J.K., Scherf, U., Bussey, K.J., Gwadry, F.G., Reinhold, W., Riddick, G.,  Pelletier, S.L., Nishizuka, S.. Szakacs, G., Annereau, J.-P. Shankavaram, U., Lababidi, S., Smith, L.H., Gottesman, M.M., and Weinstein, J.N. (2003). Comparing cDNA and oligonucleotide array data: Concordance of gene expression across platforms for the NCI-60 cancer cell lines, Genome Biology, 4, 12:R82. 
  17. Nishizuka S, Alexander J, Major SM, Scherf U, Reinhold WC, Waltham M, Charboneau L, Young L, Bussey KJ, Kim S, Lababidi S, Lee J.K., Pittaluga S, Scudiero DA, Sausville EA, Munson PJ, Petricoin EF 3rd, Liotta LA, Hewitt SM, Raffeld M, Weinstein JN. (2003). Proteomic profiling of the NCI60 cancer cell lines by using new high-density reverse-phase lysate microarrays, Proc Natl Acad Sci. 100, 24: 14229-34.
  18. Wooten GF, Currie L, Bovbjerg V, Lee J.K, and Patrie J. (2004). Aremen at greater risk for Parkinson’s disease than women? Journal of Neurology, Neurosurgery & Psychiatry, 75: 637-639.
  19. Soukup M. and Lee J.K. (2004). Optimal prediction modeling for cancer-subtype classification using gene expression data, J. of Bioinformatics and Computational Biology, 1(4): 681-694.
  20. Lee J.K., Laudeman T, Kanter J , James T., Siadaty M. , Knaus WA, Prorok A, Bao Y, Freeman B, Puiu D, Wen LM, Buck GA, Schlauch K, Weller J, and Fox JW (2004). GeneX Va: VBC Open Source Microarray Database and Analysis Software, Biotechniques, 36 (4): 634-642.
  21. Cho H. and Lee J.K. (2004). Hierarchical error model for analyzing gene expression data, Bioinformatics, 20: 2016-2025
  22. Lee J.K.(2004). Statistical Sciences in the Genomic Era: Where are we heading?Controversial Statistical Issue of ICSA Bulletin: on Bioinformatics Genomics/Proteomics, July 2004, forthcoming.
  23. Weinstein, J.N., Nishizuka, S., Reinhold, W.C., Bussey, K., Kim, S., Major, S., Lababidi, S., Feng, W., Wang, G., Raffeld, M., Sunshine, M., Narasimhan, S., Zeeberg, B., Wang, M., Lee, J.K ., and Kane, D. Cancer drug discovery: Genomics, Proteomics, and Bioinformatics. Molecular Target Therapy of Cancer, Vol. 1, in press.
  24. Mullins, I.M., Slingluff, C.L., Lee J.K., Garbee, C.F., Shu, J., Mayer, M.E., Knaus, W.A., and  Mullins,  D.W. (2004). CXCR3 Expression by Activated CD8+ T cells is Associated with Survival in Melanoma Patients with Stage III Disease, Cancer Research, 64: 7697-7701.
  25. Park T., Yi S, Lee S., Lee J.K. (2005).  Diagnostic plots for detecting outlying slides in a cDNA microarray experiment. BioTechniques 38, 463-471.
  26. Soukup M., Cho H., Lee J.K. (2005). Robust Classification Modeling on Microarray Data Using Misclassification Penalized Posterior, Bioinformatics , 21 (Suppl): i423-i430.
  27. Jain N., Cho H., O'Connell M., and Lee J.K. (2005). Rank-Invariant Resampling-based Estimation of False Discovery Rate for Analysis of Small Sample Microarray Data, BMC Bioinformatics, 6:187.

        Other Biological and Medical Topics

  1. Kang, H., Lee, J.K., and Nordheim, E.V. (1994). Number of lethal loci and lethal equivalents in Willow, Salix viminalis. Silvae Genetica, 43, 138-145. 
  2.  Lee, J.K., Nordheim, E.V., and Kang, H. (1996). Inference for lethal gene estimation with application in plants. Biometrics, 52, 451-462. 
  3.  Lee, J.K,. Lascoux, M., and Nordheim, E.V. (1996). Number of lethal equivalents in human populations: how good are the previous estimates?  Heredity, 77, 209-216.
  4. Lee, J.K., Assessment of Deleterious Gene Models via HPD Predictive p-values (1996).  Case Study: Bayesian Statistics in Science and Technology, 3, 387-397. 
  5.  Lee, J.K., Dancik, V., and Waterman, M.S. (1998). Estimation of the restriction sites observed by optical mapping using Markov Chain Monte Carlo. Journal of Computational Biology, 5, 505-515.
  6. Lascoux, M. and Lee, J.K. (1998). Characterization of deleterious loci in the fast-cycling B. napus L. base population. Genetica, 104, 161-170. 
  7. Lee, J.K., Lascoux, M., Newton, M.A., and Nordheim, E.V. (1999). A study of deleterious gene structure in plants using Markov chain Monte Carlo. Biometrics, 55, 376-386.
  8. Lee, J.K. and Thomas, D.C. (2000) Performance of Markov Chain Monte Carlo approaches for mapping genes in oligogenic models with an unknown number of loci. Am. J. Hum. Genet . 67: 1232-1250.
  9.  Lai, H.-C., Cheng, Y., Cho, H., Kosorok, M.R., and Farrell, P.M. (2004)Association Between Initial Disease Presentation, Lung Disease Outcomes, and Survival in Patients with Cystic Fibrosis, American Journal of Epidemiology , 159: 537-546.
  10. Hong, S.M., Kim, M.J., Cho, H., Pi, D.Y., Jo, D. , Yu, E., and Ro, J.Y. (2005). Superficial versus Deep Pancreatic Parenchymal Invasion in the Extrahepatic Bile Duct Carcinoma: A Significant Prognostic Factor, Modern Pathology , 18: 969-975.
  11. Hong, S.M., Cho, H., Lee, O.J., and Ro, J.Y. (2005). The Number of Metastatic Lymph Node in Extrahepatic Bile Duct Carcinoma as a Prognostic Factor, American Journal of Surgical Pathology (forthcoming).
  12. Hong, S.M., Kim, M.J., Pi, D.Y., Jo, D., Yu, E., Cho, H.,  and Ro, J.Y. (2005). Analysis of Extrahepatic Bile Duct Carcinomas according to New AJCC Staging System Focused on T Classification Problems in 222 Cases, Cancer (forthcoming).
  13. Hong S.M., Cho H., Frierson H.F., Moskaluk C.A., Yu E., Ro J.Y.
    (2005). CDX2 and MUC2 Protein Expression in Extrahepatic Bile Duct
    Carcinoma, American Journal of Clinical Pathology (forthcoming).
  14. Lee, J.W., Um, S.H., Lee, J.B., Mun, J.W., and Cho, H. (2005) Scoring and Staging Systems using Cox Linear Regression Modeling and Recursive Partitioning, Methods of Information in Medicine (forthcoming).

Book and book chapters

  1. Lee, J.K.and O’Connell, M. (2003). An Splus library for the analysis of microarray data, The analysis of gene expression data: methods and software, edited by Parmigiani, Garrett, Irizarry, and Zeger. Springer: New York.
  2. Lee, J.K., Cho, H., and  O’Connell, M. (2005). Local pooled error test for analysis of small sample microarray data, Meta-analysis and combining information in genetics , edited by David Allison and Rudy Guerra.
  3. Lee, J.K (2005). Statistical Genetics for Genomic Data Analysis, Handbook of Engineering Statistics, Edited by Hong Pham, Springer: New York.
  4. Lee, J.K. Statistical Bioinformatics: A guide for Life and Biomedical Science Researchers , John Wiley & Sons, Inc., In preparation.     

 

Proceedings and technical papers

  1. Lee, J.K, Newton, M.A., Nordheim, E.V., Kang, K. (1994). Inference on lethal gene studies via Bayesian Markov chain simulation. Computing Science and Statistics: Proceedings of the 26th Symposium on the Interface, 410-414.
  2. Lee, J.K., Newton, M.A., Nordheim, E.V., Kang, H., and Lascoux, M. (1995). Using Markov Chain Monte Carlo in practice: a case study of deleterious gene structure in plants. Technical Report 944, Department of Statistics, University of Wisconsin-Madison.
  3. Cho, H. and Loh, W.-Y. (2001). Piecewise-constant Tree-structured Modeling for Censored Data,  Technical Report 1046, Department of Statistics, University of Wisconsin-Madison
  4. Cho, H. (2002). Tree-structured Multiple Linear Regression Modeling for Censored Data,  Technical Report 1052, Department of Statistics, University of Wisconsin-Madison.
  5. Cho, H. (2002). STUDI User Manual,  Technical Report 1053, Department of Statistics, University of Wisconsin-Madison.