Jennifer Clarke

    Jennifer L. Clarke
    Professor of Statistics

    Miller School of Medicine
    University of Miami
    305-243-3022
    e-mail: bclarke2@med.miami.edu

    Higher Education

    • The Pennsylvania State University, Doctor of Philosophy in Statistics, May 2000.
    • Carnegie Mellon University, Master of Science in Statistics, May 1995.
    • Skidmore College, Bachelor of the Arts in Mathematics, May 1993.
    • Skidmore College, Bachelor of the Arts in Psychology, May 1993.

    Experience

    Academic
    • Isaac Newton Institute for Mathematical Sciences, Cambridge, UK, Invited Participant in Programme in Statistical Theory and Methods for Complex, High-Dimensional Data, January-March 2008.
    • University of Miami, Assistant Professor, Department of Medicine, 2008-present.
    • University of Miami, Assistant Professor, Department of Epidemiology and Public Health, 2007-present.
    • Duke University, Assistant Research Professor, Department of Biostatistics and Bioinformatics, 2004-2007.
    • Duke University, Assistant Research Professor, Institute of Statistics and Decision Sciences, 2005-2007.
    • Duke University, Senior Scientist, Institute for Genome Sciences and Policy, 2004-2007.
    • Duke University, Visiting Assistant Professor, Institute of Statistics and Decision Sciences, 2001-2004.
    • Indian Statistical Institute, Honorary Visiting Scientist, Machine Intelligence Unit, December 1997 – March 1998.
    • The Pennsylvania State University, Research Assistant, Department of Statistics, 1996-2000.
    • The Pennsylvania State University, Teaching Assistant, Department of Statistics, 1995-1996.

    Non-Academic
    • Proventys, Inc., Statistical Consultant. Provide guidance and direction for the design of a predictive analysis tool for the prediction of risk of disease from both biological and genomic information for the purpose of improving prospective health evaluations in a clinic setting. July 2004 – December 2004.
    • National Institute of Statistical Sciences, Research Fellow. Long-term consulting involving applied statistical research and data analysis for industrial and academic clients. Areas of research included analysis of protein assay and chemoinformatic data and the application of Bayesian model verification techniques. May 2000 – October 2001.
    • The Pennsylvania State University, Co-Director, Financial Officer, and Senior Graduate Consultant. Long and short term consulting involving research planning and data analysis for industrial and academic clients. Management of financial operations including billing and accounting. May 1999- May 2000.

    Publications

    Books and monographs published
    • Clarke, J, and Seo, D, An ensemble approach to improved prediction from multitype data, In: IMS Collections, Vol 3: Festscrift in Honor of Professor J. K. Ghosh, B Clarke and S Ghosal, Eds., Institute of Mathematical Statistics, 302-317, 2008 (refereed).

    • Pittman, J, Multilayer perceptrons and fractals, In: Encyclopedia of Computer Science and Technology, Volume 45 – Supplement 30, A Kent and J Williams, Eds., CRC Press, 177-197, 2002.

    • Pittman, J, Multilayer perceptrons and fractals, In: Encyclopedia of Microcomputers, Volume 28 – Supplement 7, A Kent and J Williams, Eds., CRC Press, 189-210, 2002.

    Juried or refereed journal articles or exhibitions
    • Berchuck, A., Iversen, E., Luo, J., Clarke, J., Horne, H., Levine, D., Boyd, J., Alonso, M., Secord, A., Bernardini, M., Barnett, J., Boren, T., Murphy, S., Dressman, H., Marks, J., and Lancaster, J. Microarray Analysis of Early Stage Serous Ovarian Cancers Shows Profiles Predictive of Favorable Outcome. Clinical Cancer Research,15, 2448-2455, 2009.

    • Webster, J. A., Gibbs, J. R., Clarke, J., Ray, M., Zhang, W., Holmans, P., Rohrer, K., Zhao, A., Marlowe, L., Kaleem, M., McCorquodale, D.S., Cuello, C., Leung, D., Bryden, L., Nath, P., Zismann, V. L., Joshipura, K., Huentelman, M. J., Hu-Lince, D., Coon, K. D., Craig, D. W., Pearson, J. V., U. S. States Alzheimer’s Disease Center Neuropathology Consortium, Heward, C. B., Reiman, E. M., Stephan, D., Hardy, J., and Myers, A. J. Genetic control of human brain transcript expression in Alzheimer’s disease. American Journal of Human Genetics, 84, 445-458, 2009.

    • Clarke, J., and West, M. Bayesian Weibull tree models for survival analysis of clinico-genomic data. Statistical Methodology, 5, 238-262, 2008.

    • Lin, X, Pittman, J, and Clarke, B. Bayesian effective samples and parameter size. IEEE Transactions on Information Theory, 53, 4438-4456, 2007.

    • Dressman, H, Berchuck, A, Chen, G, Zhai, J, Bild, A, Sayer, R, Cragun, J, Clarke, J, Whitaker, R, LiHua, L, Gray, J, Marks, J, Ginsburg, G, Potti, A, West, M, Nevins, J, and Lancaster, J, An Integrated Genomic-Based Approach to Personalized Treatment of Patients with Advanced-Stage Ovarian Cancer, Journal of Clinical Oncology, 25, 517-525, 2007.

    • Lancaster, J, Dressman, H, Clarke, J, Henriot, A, Sayer, R, Gray, J, Whitaker, R, West, M, Marks, J, Nevins, J, and Berchuck, A, Identification of genes associated with ovarian cancer metastasis using microarray expression analysis, International Journal of Gynecological Cancer, 16, 1733-1745, 2006.

    • Cheng, S, Horng, C-F, West, M, Huang, E, Pittman, J, Tsou, M-H, Dressman, H, Chen, C-M, Tsai, S, Jian, J, Liu, M-C, Nevins, J, and Huang, A, Genomic Prediction of Loco-regional Recurrence After Mastectomy in Breast Cancer. Journal of Clinical Oncology, 24, 4594-4602, 2006.

    • Cheng, S., Horng, C.-F., Clarke, J., Tsou, M.-H., Chen, C.-M., West, M., Nevins, J., and Huang, A. Prognostic index score and clinical prediction model of local regional recurrence after mastectomy in breast cancer patients, International Journal of Radiation Oncology, Biology, Physics, 64, 1401-1409, 2006.

    • Berchuck, A, Iversen, E, Lancaster, J, Pittman, J, Luo, J, Lee, P, Murphy, S, Dressman, H, Febbo, P, West, M, Nevins, J, and Marks, J, Patterns of gene expression that characterize long-term survival in advanced stage serous ovarian cancers, Clinical Cancer Research, 11, 3686-3696, 2005.

    • Sayer, R., Lancaster, J., Pittman, J., Gray, J., Whitaker, R., Marks, J., and Berchuck, A. (2005). High insulin-like growth factor-2 (IGF-2) gene expression is an independent predictor of poor survival in advanced stage serous epithelial ovarian cancer. Gynecologic Oncology, 96, 355-361.

    • Pittman, J, Huang, E, Dressman, H, Horng, C-F, Cheng, S, Tsou, M-H, Chen, C-M, Bild, A, Iversen, E, Huang, A, Nevins, J, and West, M, Clinico-genomic models for personalized prediction of disease outcomes, PNAS, 101, 22, 8431-8436, 2004.

    • Pittman, J, Huang, E, Nevins, J, and West, M, Bayesian analysis of binary prediction tree models for retrospectively sampled outcomes, Biostatistics, 5, 4, 587-601, 2004.

    • Tebbit, C., Marks, J., Dressman, H., Blanchette, C., Iverson, E., Pittman, J., and Olson, J. Gene expression signature characterizing cyclin E protein overexpression in primary breast tumors. Journal of the American College of Surgeons, 199, S1, 78-79, 2004.

    • Seo, D, Dressman, H, Hergerick, E, Iversen, E, Dong, C, Vata, K, Milano, C, Rigat, F, Pittman, J, Nevins, J, West, M, and Goldschmidt-Clermont, P, Gene expression phenotypes of atherosclerosis, Atherosclerosis, Thrombosis, and Vascular Biology, 24, 1922-1927, 2004.

    • Huang, E, Cheng, S, Dressman, H, Pittman, J, Tsou, M-H, Horng, C-F, Bild, A, Iversen, E, Liao, M, Chen, C-M, West, M, Nevins, J, and Huang, A, Gene expression predictors of breast cancer outcomes, The Lancet, 361, 1590-1596, 2003.

    • Nevins, J, Huang, E, Dressman, H, Pittman, J, Huang, A, and West, M, Towards integrated clinico-genomic models for personalized medicine: combining gene expression signatures and clinical factors in breast cancer outcomes prediction, Human Molecular Genetics, 12, R153-R157, 2003.

    • Huang, E, Ishida, S, Pittman, J, Dressman, H, West, M, and Nevins, J, Gene expression phenotypic models that predict the activity of oncogenic pathways, Nature Genetics, 34, 2, 226-230, 2003.

    • Pittman, J, Adaptive splines and genetic algorithms, Journal of Computational and Graphical Statistics, 11, 3, 1-24, 2002.

    • Pittman, J, Sacks, J, and Young, S, The construction and assessment of a statistical model for the prediction of protein assay data, Journal of Chemical Information and Computer Science, 42, 3, 729-741, 2002.

    • Pittman, J, and Murthy, C, Fitting optimal piecewise linear functions using genetic algorithms, IEEE Pattern Analysis and Machine Intelligence, 22, 7, 701-718, 2000.

    • Murthy, C, and Pittman, J, Multilayer perceptrons and fractals, Information Sciences, 112, 1, 137-150, 1998.

     

    Other works, publications and abstracts
    • Clarke, B., and Clarke, J. Unsubmitted: Thoughts on Refereeing, Institute of Mathematical Statistics Bulletin, 38, 6, 8-9, July 2009.

    • Pittman, J, The importance of validation in genomic studies of breast cancer, Breast Diseases: A Yearbook Quarterly, 16, 16-19, 2005.

    • Pittman, J, Huang, E, Nevins, J, and West, M, Prediction tree models in clinico-genomics, Bulletin of the International Statistical Institute, 54, 76, 2003.

    • Pittman, J, Adaptive Splines and Genetic Algorithms for Optimal Statistical Modeling, Thesis for Doctor of Philosophy. Advisor, C.R. Rao, 2000.

    • Pittman, J. Adaptive Splines and Genetic Algorithms. In Proceedings of the Computational and Graphical Statistics Section, 2000 Joint Statistical Meetings, Baltimore, MD. Alexandria, VA: American Statistical Association.

    • Pittman, J., and Murthy, C.A. Fitting robust optimal piecewise linear functions via genetic algorithms. In Third International Workrhop on Frontiers in Evolutionary Algorithms (FEA '2000), In JCIS 2000 Proceedings, Atlantic City, NJ, 2000. Association for Intelligent Machinery.

     

    Other works accepted for publication
    • Clarke, J. and Clarke, B. Prequential analysis of complex data with adaptive combined average predictors. Statistical Analysis and Data Mining, accepted for publication, July 2009.

    • Hnatyszyn, J., Iorns, E., Seo, P., Clarke, J., Ward, T., and Lippman, M. SATB1 is not a critical protein for human breast cancer growth, progression and metastasis, Cancer Cell, submitted for publication, July 2009.

    • Seo, D., Clarke, J., Slosek, K., Shah, S., Donahue, M., Sketch, M., Newby, K., Ginsburg, G., Granger, C., Kraus, W., and Goldschmidt-Clermont, P. (2008), A blood test for coronary artery disease: Using blood gene expression to detect coronary atherosclerosis. American Journal of Cardiology, submitted for publication.