Devin C. Koestler, Ph.D.
Associate Professor, Department of Biostatistics
Academic Editor, PLOS ONE
Associate Director, Biostatistics and Informatics Shared Resource, The University of Kansas Cancer Center
B.S., Applied Mathematics, Rochester Institute of Technology, Rochester, NY
Ph.D., Biostatistics, Brown University, Providence, RI
Post-Doc, Quantitative Biosciences in Cancer, Dartmouth College, Hanover, NH
Graduate Certificate, Bioinformatics, Stanford University Center for Professional Development Anticipated Completion (Fall 2015)
2011 - Eastern North American Region (ENAR) Distinguished Student Paper Award
2011 - Ruth L. Kirschstein National Research Service Awardee (NRSA)
2015 - Department of Biostatistics Outstanding Graduate Teaching Award Recipient
High-dimentional genomic data, statistical genomics, mixture models, clustering and classification, molecular epidemiology, epigenetics, and DNA methylation.
The broad mission of my research involves the development and application of bioinformatics/statistical methodologies for analyzing high-throughput 'omic' data. I also have deeply rooted interest in epigenetics and molecular epidemiology, specifically DNA methylation and its implications for human health and disease. Depending on the disease or condition being studied, its possible that only a small fraction of the molecular markers measured (i.e., CpG sites, genes, etc.) vary across subjects in any biologically meaningful way. My job is therefore to develop new and/or apply existing statistical methodologies for identifying these markers and to understand their functional role in the context of the disease under study. An appropriate analogy for this task is the age-old adage, "finding a needle in a haystack" - actually it is often like trying to find a needle in a barn full of haystacks! In addition to my methodological interests, which include, multivariate statistics, mixture models, and mixed-effects models, I am also passionate about my collaborations, which span from environmental health, the human microbiome, to a wide variety of different epigenetics studies. The shared theme across my collaborative research projects is the use of high-dimensional genomic data to gain further insight into some biological process.
Scholarly Activity and Academic Credentials
In the News and Web Coverage of Research
2014 - Feature story in the University of Kansas Cancer Center (KUCC) newsletter (http://www.kucancercenter.org/cancer-research-and-education/at-the-bench/math-model-prediction)
2014 - Statistics bootcamp: estimating pi with R and Buffon's needle. Significance Magazine. Mentored graduate student Eric Wika in the preparation of this article. (http://www.statslife.org.uk)
2014 - Accelerating ovarian cancer drug discovery using bioinformatics. AAPS blog post. (http://aapsblog.aaps.org/tag/devin-c-koestler/)
2013 - Featured in 2013 issue of AMSTAT news, "Post-doctoral Fellowships, Programs, and Opportunities" (http://magazine.amstat.org)
2012 - Featured on the cover of the August 2012 issue of Cancer Epi Bio Prev and described by the editor in that issue's highlights.
- Covered as a press release in Dartmouth Now, Dartmouth's source of news and noteworthy research discoveries.
- Described in an article published in The Dartmouth, the nation's oldest college newspaper.
- Listed as an example of research among the top reasons prospective MPH students should consider Dartmouth College.
- Featured in Epigenie, a repository of highlights in epigenetics research.
1. Koestler DC. Semi-supervised methods for analyzing high-dimensional genomic data. Statistical Diagnostics of Cancer: Analyzing High-Dimensional Genomic Data. Dehmer M (Editor) and Emmert-Streib F (Series Editor). Wiley-Blackwell (2013). ISBN: 978-3-527-33262-5
2. Koestler DC and Houseman EA. Model based clustering analysis of DNA methylation array data. Computational and Statistical Epigenomics. Teschendorff A (Editor) Springer: Translational Bioinformatics Series (Due June 2015). ISBN 978-94-017-9926-3
Top 15 Publications
1. Koestler D.C., Marsit C.J., Christensen B.C., Karagas M.R., Bueno R., Sugarbaker D.J., Kelsey K.T. & Houseman E.A. (2010). Semi-supervised recursively partitioned mixture models for identifying cancer subtypes. Bioinformatics, 26(20), 2578-85. PMID: 20834038.
2. Marsit C.J., Koestler D.C., Christensen B.C., Karagas M.R., Houseman E.A. & Kelsey K.T. (2011). DNA methylation array analysis identifies profiles of blood-derived DNA methylation associated with bladder cancer. Journal of Clinical Oncology, 29(9), 1133-9. PMID: 21343564.
3. Christensen B.C., Smith A., Zheng S., Koestler D.C., Houseman E.A., Marsit C.J., Wiemels J.L., Nelson H.N., Karagas M.R., Wrensch M.R., Kelsey K.T. & Wiencke J.K. (2010). DNA methylation, isocitrate dehydrogenase mutation, and survival in glioma. Journal of the National Cancer Institute, 103(2), 143-53. PMID: 21163902.
4. Avissar-Whiting M., Koestler D.C., Houseman E.A., Christensen B.C., Kelsey K.T. & Marsit C.J. (2011). Polycomb group genes are targets of aberrant DNA methylation in renal cell carcinoma. Epigenetics, 6(6), 703 -9. PMID: 21610323.
5. Langevin S.M., Koestler D.C., Christensen B.C., Wiencke J.K., Nelson H., Houseman E.A., Marsit C.J. & Kelsey K.T. (2012). DNA methylation profiles in peripheral blood are predictive of head and neck squamous cell carcinoma. Epigenetics, 7(3), 291-9. PMID: 22430805.
6. Houseman E.A., Accomando W., Koestler D.C., Christensen B.C., Kelsey K.T. & Wiencke J.K. (2012). DNA methylation arrays as a surrogate measure of cell mixtures. BMC Bioinformatics, doi: 10.1186/1471-2105-13-86. PMID: 22568884.
7. Madan J., Koestler D.C., Stanton B., Davidson L., Moore J.H., Sogin M., Saxena D., Hampton T., Palumbo P., Guill M., Karagas M.R., O'Toole G.A. & Hibberd P.H. (2012). The developing respiratory and intestinal microbiome in cystic fribrosis infancy. MBio, doi:pii: e00251-12. 10.1128/mBio.00251-12. PMID: 22911969.
8. Koestler D.C., Marsit C.J., Christensen B.C., Langevin S.M., Accomando W., Houseman E.A., Karagas M.R., Wiencke J.K. & Kelsey K.T. (2012). Peripheral blood immune cell methylation profiles are associated with non-hematopoietic cancers. Cancer Epidemiology Biomarkers & Prevention. 21(8), 1293-302. PMID: 22714737.
9. Koestler D.C., Christensen B.C., Marsit C.J., Kelsey K.T. & Houseman E.A. (2013). Recursively partitioned mixture model clustering of DNA methylation data using biologically informed correlation structures. Statistical Applications in Genetics and Molecular Biology, [Epub ahead of print]. PMID: 23468465.
10. Cicek M.S., Koestler D.C., Fridley B.R., Armasu, S.M., Kalli K.R., Winterhoff B.R., Chien J., Fan J., Bibikova M., Block M.A., Olson J.E., Charbonneau B., Shridhar V., Cunningham J.M. & Goode E.L. (2013). Ovarian cancer methylation profiles vary by histological subtype. Human Molecular Genetics, [Epub ahead of print]. PMID: 23571109.
11. Koestler D.C.#, Li J, Baron J, Dietrich A, Tsongalis G, Butterly L, Goodrich M, Lesseur C, Karagas M.R., Marsit CJ, Moore JH, Andrew A, Srivastava A. (2013). Differential methylation of colon adenomas of the right side. Modern Pathology. [Epub ahead of print]. PMID: 23868178.
12. Koestler DC#, Christensen BC#, Karagas MR, Marsit CJ, Langevin SM, Kelsey KT, Wiencke JK, Houseman EA. (2013). Blood based patterns of DNA methylation predict the underlying distribution of cell types: a validation analysis. Epigenetics, 8(8), 816-26. PMID: 23903776.
13. Koestler DC, Ombao H , and Bender J. (2013). Ensemble-based methods for forecasting census in hospital units. BMC Medical Research Methodology, doi: 10.1186/1471-2288-13-67. PMID: 23721123.
14. Koestler DC, Avissar-Whiting, Karagas MR, and Marsit CJ. (2013). Differential DNA methylation in umbilical cord blood of infants exposed to low levels of arsenic in-utero. Environmental Health Perspectives, 121(8), 971-7. PMID: 23757598.
15. Wilhelm-Benartzi C#, Koestler DC#, Karagas MR, Flanagan JM, Christensen BC, Kelsey KT, Marsit CJ, Houseman EA, and Brown R. Good practice in DNA methylation array processing and analysis. British Journal of Cancer. [In press].
# - Authors contributed equally to this work.