Carnegie Mellon University

Biography

Rebecca Doerge is dean of the Mellon College of Science at Carnegie Mellon University and a member of the Dietrich College of Humanities and Social Sciences' Department of Statistics and the Mellon College of Science’s Department of Biological Sciences.

Doerge's research program focuses on statistical bioinformatics, an interdisciplinary component of bioinformatics that brings together many scientific disciplines for the purpose of asking, answering, and disseminating biologically interesting information in the quest to understand the ultimate function of DNA and epigenomic associations.

Doerge is an elected Fellow of the American Statistical Association (2007) and the American Association for the Advancement of Science (2007), and a Fellow of the Committee on Institutional Cooperation (2009). She declined the American Council on Education Fellowship in 2016 to become dean of the Mellon College of Science. She is also a member of the Board of Trustees for the National Institute of Statistical Sciences and the Mathematical Biosciences Institute; a member of the Engineering External Review Committee at Lawrence Livermore National Laboratory; and a member of the Global Open-Source Breeding Informatics Initiative Advisory Board.

She has published two books and more than 120 scientific articles. She has mentored many students, including 24 doctoral students who have successfully defended their theses.

Doerge was born and raised in upstate New York. As a first generation student, she studied theoretical mathematics at the University of Utah. It was there that she gained interest and experience in both computing and human genetics. Doerge obtained her Ph.D. in statistics from North Carolina State University under the direction of Bruce Weir. She was a postdoctoral fellow with Gary Churchill at Cornell University, studying biometry and plant breeding.

Prior to joining Carnegie Mellon University, Doerge was the Trent and Judith Anderson Distinguished Professor of Statistics at Purdue University. She joined Purdue University in 1995 and held a joint appointment between the Colleges of Agriculture (Department of Agronomy) and Science (Department of Statistics). She was the recipient of Purdue’s Teaching for Tomorrow Award (1996), University Scholar Award (2001-06), and Provost's Award for Outstanding Graduate Faculty Mentor (2010).

B.S. in Mathematics, 1982-1986
University of Utah, Salt Lake City, Utah
M.Stat. in Mathematics, 1986-1988
University of Utah, Salt Lake City, Utah
Advisor: Simon Tavaré
Thesis: Information of Fixed Cluster Samples for Genetic Traits Involving Mixtures of Distributions
Ph.D. in Statistics, 1989-1993
North Carolina State University, Raleigh, North Carolina
Minor in Genetics
Advisor: Bruce Weir
Dissertation: Statistical Methods for Locating Quantitative Trait Loci with Molecular Markers
Postdoctoral Fellow, 1993-1995
Cornell University, Ithaca, New York
Sponsor: Gary Churchill (Department of Plant Breeding and Biometry)

8/1990 to 12/1992 - NSF RESEARCH FELLOW - North Carolina State University, Statistics Department

12/1992 to 5/1993 - RESEARCH ASSISTANT - North Carolina State University, Statistics Department

5/1993 to 7/1993 - POSTDOCTORAL ASSOCIATE - North Carolina State University, Statistics Department: Dr. Bruce Weir

8/1993 to 7/1995 - INSTRUCTOR/POSTDOCTORAL ASSOCIATE - Cornell University, Biometrics Unit: Dr. Gary Churchill

8/1995 to 8/2000 - ASSISTANT PROFESSOR OF STATISTICS (75%) and AGRONOMY (25%) - Purdue University

8/2000 to 8/2003 - ASSOCIATE PROFESSOR OF STATISTICS AND AGRONOMY - Purdue University

8/2003 to 08/2016 - PROFESSOR OF STATISTICS AND AGRONOMY - Purdue University

8/2008 to 7/2009 - INTERIM HEAD OF STATISTICS - Purdue University, Department of Statistics

7/2009 to 6/2010 - ASSOCIATE HEAD OF STATISTICS - Purdue University, Department of Statistics

7/2010 to 6/2015 - DEPARTMENT HEAD OF STATISTICS - Purdue University, Department of Statistics

10/2011 to 8/2016 - TRENT AND JUDITH ANDERSON DISTINGUISHED PROFESSOR OF STATISTICS

8/2016 to Present - DEAN OF MELLON COLLEGE OF SCIENCE - Carnegie Mellon University

12/2017 to Present - GLEN DE VRIES DEAN'S CHAIR IN THE MELLON COLLEGE OF SCIENCE

1993-1995 Cornell University, Biometrics Unit
Course: Introduction to Statistical Methods
Text: Devore and Peck
1993-1995 Cold Spring Harbor Laboratory Course - Cold Spring Harbor, NY
Molecular Markers for Plant Genetics and Plant Breeding (with Ben Burr and Scott Tingey)
1995-2002 Purdue University, Statistics Dept
Courses: Applied Regression Analysis (service course for non-majors (ST512), graduate level statistics course (ST525))
Text: Neter, Kutner, Nachtsheim, and Wasserman
1995-2005 The (abroad) Summer Institute in Statistical Genetics - North Carolina State University, Raleigh, NC
1996 The International Potato Center - Lima, Peru
Molecular Markers for Potato Germplasm Management and Enhancement Course (with Scott Tingey)
1998 Purdue University, Statistics Dept
Course: Introduction to Statistics and Probability (ST511)
Text: Devore
1999-2016 (every other year) Purdue University
Course: An Applied Introduction to QTL Mapping in Experimental Populations (STAT 549)
Text: Lynch and Walsh
1999-2016 Purdue University, Statistics Dept
Course: Bioinformatics/Statistical Bioinformatics Seminar Series.
2003 Purdue University, Statistics Dept
Discovering Genomics, Proteomics, and Bioinformatics
Text: Campbell and Heyer
2005 Purdue University, Statistics Dept
Course: Applied Regression Analysis (ST525)
Text: Kutner, Nachtsheim, Neter, and Li
2006-2016 The (abroad) Summer Institute in Statistical Genetics - University of Washington, Seattle, WA
2010-2015 Purdue University
First Year Graduate Student Seminar. Fall semesters only
  • American Society of Plant Biologists
  • American Association for the Advancement of Science
  • American Statistical Association
  • Genetics Society of America
  • International Biometric Society
  • Institute of Mathematical Statistics
External departmental reviews:
  • 2002 (Chair) University of Minnesota, Program in Biostatistics
  • 2007 University of Nevada-Reno, Department of Biochemistry (USDA-review)
  • 2010 Statistical and Applied Mathematical Sciences Institute (SAMSI; NSF-review)
  • 2013 University of Nebraska-Lincoln, Department of Statistics
  • 2015 University of Pittsburgh, Department of Statistics
Federal grant review panel:
  • 1997 United States Department of Agriculture Plant Genome Panel
  • 1999 United States Department of Agriculture Animal Genetic Mechanisms Panel
  • 2000 National Science Foundation Biocomplexity Panel
  • 2001 United States Department of Agriculture (IFAFs) Panel
  • 2002 United States Department of Agriculture (NRI) Bioinf. Panel Manager
  • 2006 National Institute of Health (NIH) Software Maintenance and Dev. Panel
  • 2012 National Science Foundation Biology; Plant Genome Panel
  • 2015 National Science Foundation Division of Mathematical Sciences Panel
Grant reviews for:
  • USDA, NSF, NIH, Welcome Trust, Howard Hughes
Manuscript reviews for:
  • Biometrics, Cell, Crop Science, Evolution, Genetics, Genetical Research
  • Genome Research, JASA, Journal of Quantitative Trait Loci, Molecular Breeding
  • Nature, Nature Reviews Genetics, Plant Breeding Reviews
  • Plant Physiology, Plant Cell, PLoS One, Science, Statistical Science
  • Statistical Applications in Genetics and Molecular Biology, Theoretical and Applied Genetics
  • Theoretical and Population Biology, Trends in Genetics
  • The Plant Cell, The Proceedings of the National Academy of Sciences USA
Book review for:
  • 1999 Applied Linear Regression Models, Fourth Edition. Authors: Neter, Kutner, Nachtsheim, and Wasserman
  • 2006 Bioinformatics and Computational Biology Solutions Using R and Bioconductor. Authors: Gentleman, Carey, Huber, Irizarry, and Dudoit (eds): Biometrics. 62:4 (1270-1271)
  • 2009 A Guide to QTL Mapping with R/qtl. Authors: Broman and Sen. Biometrics (invited)
Conference organization/participation:
  • Invited talks for major Genetics, Plant Breeding, and Statistical conferences
  • Organized Statistical Genetics session for the 1996, 1997 Joint Statistical Meetings
  • 1998 Organized the Statistical Genetics Workshop, 6th Purdue Symposium on Statistics
  • 1998-2005 Organizing Committee for The International Plant and Animal Genome Meeting, San Diego, CA
  • 2003 Co-Chair, Gordon Conference on Quantitative Genetics and Genomics, Ventura, CA
  • 2003 Organized the Bioinformatics and Microarray Workshop, 7th Purdue Symposium on Statistics
  • 2005 Chair, Gordon Conference on Quantitative Genetics and Genomics, Ventura, CA
  • 2009 Co-Chair (with Jaya Satagopan), Joint Statistics Meeting (JSM) session on Epigenomics, Washington DC
  • 2009-2012 Member of the Statistical Practice Conference Planning Committee, American Statistical Association (2012)
  • 2010-2012 Member, International Advisory Committee (IAC) for the Fourth International Conference on Quantitative Genetics, Edinburgh, Scotland; June 2012
  • 2011-2012 Member, Organizing and Program Committee for the 8th International Purdue Symposium on Statistics "Diversity in the Statistical Sciences for the 21st Century", West Lafayette, IN; June 2012
  • 2013 Member, Organizing Committee "Impact of Large-Scale Genomic Data on Statistical and Quantitative Genetics Conference", Seattle, WA; November 2013
  • 2014-2016 Member, International Advisory Committee (IAC) for the Fifth International Conference on Quantitative Genetics, University of Wisconsin, Madison; June 2016
  • 1996-2000 Co-Editor, Journal of Agricultural Genomics (JAG) http://www.ncgr.org/ag/jag/
  • 2002-2012 Associate Editor, Statistical Applications in Genetics and Molecular Biology http://www.bepress.com/sagmb/
  • 2003-2009 Associate Editor, GENETICS http://www.genetics.org
  • 2003-2008 Associate Editor, The Plant Cell  http://www.plantcell.org
  • 2006-2012 University of Florida Genomics Institute Advisory Board (Advisors to Ken Burns)
  • 2006-2010 American Association for Cancer Research Epigenomics Task Force (Advisors to Peter Jones)
  • 2007-2010 Samuel S. Wilks Memorial Medal Committee of the American Statistical Association
  • 2007-2012 Cold Spring Harbor Laboratory External Advisory Board on Quantitative Biology
  • 2008-2013 Associate Editor, Genetics Research
  • 2008-present Associate Editor, Epigenomics
  • 2009-2012 Advisory Board (University of South Carolina) NSF ESPCoR Cyberinfrastructure research Infrastructure project (PI: Jim Bottom)
  • 2010-2015 Advisory Board (German Ministry of Research and Education) Synbreed: Synergistic plant and animal breeding (PI: Chris Schoen)
  • 2010-2012 Cavell Brownie Scholars Mentoring Program Committee
  • 2011-2015 American Statistical Association Committee on Women in Statistics
  • 2011-present Associate Editor, G3: Genes|Genomes|Genetics
  • 2012-present Member, Board of Trustees, National Institute of Statistical Sciences (NISS)
  • 2012 American Statistical Association Gertrude Cox Scholarship Award Committee
  • 2012 National Institute of Statistical Sciences Jerome Sacks Award Committee
  • 2013-present Member, Statistical and Mathematical Sciences Institute (SAMSI) National Advisory Committee
  • 2013-2014 Chair, American Statistical Association Gertrude Cox Scholarship Award Committee
  • 2014-present Member, Board of Trustees Mathematical Biosciences Institute, The Ohio State University
  • 2014 Chair, National Institute Statistical Science Awards Committee
  • 2014-present Associate Editor, Journal of the American Statistical Association (JASA) Theory and Methods
  • 2015 Snedecor Awards Committee of the American Statistical Association
  • 2015-2019 Advisory Board, Global Open-Source Breeding Informatics Initiative (GOBII), Cornell University
  • 1990-1993 NSF Fellowship in Mathematics and Molecular Biology (UC Berkeley)
  • 1990-1992 Gertrude Cox Fellowship (NC State University)
  • 1991 Mu Sigma Rho membership (NC State University)
  • 1992 Cold Spring Harbor Laboratory award to attend Molecular Markers for Plant Breeding
  • 1994 Instit. for Math. and its Appl. award to attend the Mol. Bio. program (Univ. MN)
  • 1996 Teaching for Tomorrow Award (Purdue University)
  • 1997 Outstanding Asst Prof. for Excellence in Teaching and Research (Science, Purdue)
  • 1998 Outstanding Teacher of Undergrads, School of Science (Purdue University)
  • 1998-1999 Who's Who Among America's Teachers (student nominated, Purdue University)
  • 2001 Elected Member Gamma Sigma Delta
  • 2002 James Madison University Visiting Scholar
  • 2001-2006 University Scholar (Purdue University)
  • 2007 College of Science Graduate Student Mentoring Award (Purdue University)
  • 2007 Elected Member Sigma Xi
  • 2007 Elected Fellow of the American Statistical Association
  • 2007 Elected Fellow of the American Association for the Advancement of Science (AAAS)
  • 2009 Fellow, Committee on Institutional Cooperation (CIC)
  • 2010 Provost's Award for Outstanding Graduate Faculty Mentor (Purdue University)
  • 2011 Trent and Judith Anderson Distinguished Professor of Statistics (Purdue University)
  • 2015 College of Science Leadership Award (Purdue University)
  • 2017 Glen de Vries Dean’s Chair in the Mellon College of Science (Carnegie Mellon University)

Google Scholar Citation List

Refereed Book Chapters, Proceedings, and Publications (130)

Books (2); Reviewed Book Chapters (7); Reviewed Proceedings (29); Journal Publications (92)
Current and former Purdue graduate students denoted by an asterisk (*).

[1] G.A. Churchill and R.W. Doerge. 1994. Empirical threshold values for quantitative trait mapping. Genetics. 138:963-971.

[2] R.W. Doerge. 1995. Testing for linkage: phase known/phase unknown. Journal of Heredity. 86(1):61-62.

[3] R.W. Doerge. 1995. The relationship between the LOD score and the analysis of variance F-statistic when detecting QTL using single markers. Appendix 1: Locating genes associated with root morphology and drought avoidance in rice via linkage to molecular markers. M.C. Champoux, G. Wang, S. Sarkarung, D.J. Mackill, J.C. O'Toole, N. Huang, S.R. McCouch. Theoretical and Applied Genetics. 90:969-981.

[4] S.R. McCouch and R.W. Doerge. 1995. QTL mapping in rice. Trends in Genetics. 11(12):482-487.

[5] R.W. Doerge and G.A. Churchill. 1996. Permutation tests for multiple loci affecting a quantitative character. Genetics. 142:285-294.

[6] R.W. Doerge and A. Rebaï. 1996. Signi cance thresholds for QTL interval mapping tests. Heredity. 76:459-464.

[7] M.A. Mutschler, R.W. Doerge, J.P. Kuai, S.C. Liu, B. Liedl, and Y. Shapiro. 1996. QTL analysis of the production of acylsugars responsible for pest resistance in the wild tomato lycopersicon pennellii. Theoretical and Applied Genetics. 92:709-719.

[8] R.W. Doerge. 1996. Constructing genetic maps by rapid chain delineation. Journal of Quantitative Trait Loci. Volume 2. Article 6. http://probe.nalusda.gov:8000/otherdocs/jqtl

[9] R.W. Doerge, Z-B. Zeng, and B.S. Weir. 1997. Statistical issues in the search for genes affecting quantitative traits in experimental populations. Statistical Science. 12(3):195-219.

[10] C. Teuscher, D.M. Rhein, K.D. Livingstone, R.A. Paynter, R.W. Doerge, S.M. Nicholson, and R.W. Melvold. 1997. Evidence that Tmevd2 and eae3 may represent either a common locus or gene complex controlling susceptibility to immunologically mediated demyelination in mice1. Journal of Immunology. 159:4930-4934.

[11] G.A. Churchill and R.W. Doerge. 1997. Mapping Quantitative Trait Loci in Experimental Populations. In: Molecular Dissection of Complex Traits. A.H. Paterson (ed). CRC Press: New York.

[12] R.J. Roper, R.W. Doerge, S.B. Call, K.S.K. Yung, W.F. Hickey, and C. Teuscher. 1998. Autoimmune orchitis, epididymitis, and vastis are immunogenetically distinct lesions. The American Journal of Pathology. 152(5):1337-1345.

[13] R.J. Roper, J.S. Griffith, C.R. Lyttle, R.W. Doerge, A.W. McNabb, R.E. Broadbent, and C. Teuscher. 1998. Interacting quantitative trait loci control phenotypic variation in murine estradiol-regulated responses. Endocrinology. 2(140):556-561.

[14] R.W. Doerge. 1998. Statistical threshold values for locating quantitative trait loci. Proceedings of the Tenth Annual Conference on Applied Statistics in Agriculture, Kansas State University. Edited by George Milliken. 10:84-95.

[15] J. Weis, B. McCracken, Y. Ma, D. Fairbairn, R. Roper, J. Weis, J. Zachery, R.W. Doerge, and C. Teuscher. 1999. Identi cation of quantitative trait loci governing arthritis severity and humoral responses in the murine model of Lyme disease. Journal of Immunology. 162:948-956.

[16] R.J. Butter eld, E.P. Blankenhorn, R.J. Roper, J.F. Zachary, R.W. Doerge, J. Sudweeks, J. Rose, and C. Teuscher. 1999. Genetic analysis of disease subtype and sexual dimorphism in mouse EAE: Relapsing-remitting and monophasic remitting/non-relapsing EAE are immunogenetically distinct. Journal of Immunology. 162(5):3096-3102.

[17] S.A. Fennimore, G.E. Shaner, W.E. Nyquist, R.W. Doerge, and M.E. Foley. 1999. A genetic model and molecular markers for wild oat (Avena fatua L.) seed dormancy. Theoretical and Applied Genetics. (3-4):711-718.

[18] C. Teuscher, R.J. Butter eld, R. Ma, J. Zachary, R.W. Doerge, and E.P. Blankenhorn. 1999. Sequence polymorphisms in the chemokines scya1 (TCA-3), scya2 (Monocyte chemattractant protein (MCP-1)), and scya12 (MCP-5) are candidate genes for eae 7, a locus controlling the susceptibility to monophasic remitting/nonrelapsing experimental allergic encephalomyelitis. Journal of Immunology. 163:2262-2266.

[19] D. Nettleton and R.W. Doerge. 2000. Accounting for variability in the use of permutation testing to detect quantitative trait loci. Biometrics. 56:285-291.

[20] R. Bernardo, J. Romero-Severson, J. Ziegle, J. Hauser, L. Joe, G. Hookstra, and R.W. Doerge. 2000. Parental contribution and coefficient of coancestry among maize inbreds: Pedigree, RFLP, and SSR data. Theoretical and Applied Genetics. 100:552-556.

[21] E.P. Blankenhorn, R.J. Butter eld, R. Rigby, L. Cort, D. Giambrone, P. McDermott, K. McEntee, N. Solowski, N.D. Meeker, J.F. Zachary, R.W. Doerge, and C. Teuscher. 2000. Genetic analysis of the in uence of pertussis toxin in EAE susceptibility: an environmental agent can override genetic checkpoints. The Journal of Immunology. 164(6):3420-3425.

[22] R.W. Doerge and Bruce A. Craig. 2000. Model selection for quantitative trait locus analysis in polyploids. Proceedings of the National Academy of Science. 97(14):7951-7956.

[23] R.J. Butter eld, E.P. Blankenhorn, R.J. Roper, J.F. Zachary, R.W. Doerge, and C. Teuscher. 2000. Genetic analysis of the histopathology of murine Experimental Allergic Encephaolmyelitis (EAE): identi cation of brain, spinal cord, and gender-speci c loci controlling lesion formation and severity. American Journal of Pathology. 157(2):637-646.

[24] R.W. Doerge and Bruce A. Craig. 2000. An introduction to model selection for quantitative trait locus analysis in polyploids. Proceedings of Applied Statistics in Agriculture, Kansas State University. Edited by George Milliken, pp13-27.

[25] L.M. McIntyre, C. Coffman, and R.W. Doerge. 2001. Detection and location of a single binary trait locus in experimental populations. Genetical Research. 78:79-92.

[26] R.J. Roper, J.J. Weis, B.A. McCracken, C.B. Green, Y. Ma, K.S. Weber, D. Fairbairn, R.J. Butter eld, M.R. Potter, J.F. Zachary, R.W. Doerge, and C. Teuscher. 2001. Susceptibility to experimental lyme arthritis is linked to multiple loci on chromosome 5 in four independent mouse crosses. Genes and Immunity. 2(7):388-397.

[27] R.W. Doerge. 2001. Quantitative Trait Loci. Plant Sciences for Students. Macmillan Reference USA, pp195-196.

[28] J. Wilbur*, J.K. Ghosh, C.H. Nakatsu, S.M. Brouder, and R.W. Doerge. 2001. Statistical issues in the analysis of microbial communities in soil. Proceedings of Applied Statistics in Agriculture, Kansas State University. Edited by George Milliken, pp129-143.

[29] M.A. Black* and R.W. Doerge. 2001. Calculation of the minimum number of replicate spots required for detection of signi cant gene expression fold changes for cDNA microarrays. Proceedings of Applied Statistics in Agriculture, Kansas State University. Edited by George Milliken, pp144-158.

[30] B.A. Craig, O. Vitek*, M.A. Black*, M. Tanurdzic, and R.W. Doerge. 2001. Designing microarray experiments: chips, dips, ips, and skips. Proceedings of Applied Statistics in Agriculture, Kansas State University. Edited by George Milliken, pp159-182.

[31] R.W. Doerge. 2002. Mapping and analysis of quantitative trait loci in experimental populations. Nature Reviews Genetics. 3:43-52.

[32] J. Wilbur*, J.K. Ghosh, C.H. Nakatsu, S.M. Brouder, and R.W. Doerge. 2002. Variable selection in high-dimensional multivariate binary data with application to the analysis of microbial community DNA ngerprints. Biometrics. 58:378-386.

[33] R.J. Roper, R.Z. Ma, J.E. Biggins, R.J. Butter eld, S.D. Michael, K.S.K. Tung, R.W. Doerge, and C. Teuscher. 2002. Interacting quantitative trait loci control loss of peripheral tolerance and susceptibility to autoimmune ovarian dysgenesis after day three thymectomy in mice. Journal of Immunology. 169:1640-1646.

[34] M. Black* and R.W. Doerge. 2002. Calculation of the minimum number of replicate spots required for detection of signi cant gene expression fold change in microarray experiments. Bioinformatics. 18(12):1609-1616.

[35] R.J. Butterfield, R.J. Roper, D.M. Rhein, R.W. Melvold, L.Haynes, R.Z. Ma, R.W. Doerge, and C. Teuscher. 2002. Sex speci c QTL govern susceptibility to Theiler's murine encephalomyelitis virus-induced demyelination (TMEVD). Genetics. 163(3):1041-1046.

[36] B.A. Craig, M.A. Black*, and R.W. Doerge. 2003. Gene Expression: The technology and statistical analysis. JABES. 8(1):1-28.

[37] T.C. Osborn, J.C. Pires, J.A. Birchler, Z.J. Chen, L. Comai, R.W. Doerge, and R.A. Martienssen. 2003. Understanding the causes of novel variation in polyploids. Trends in Genetics. 19(3):141-147.

[38] Veena, H. Jiang*, R.W. Doerge, and S.B. Gelvin. 2003. Differential expression of plant genes during the initial stages of Agrobacterium-mediated transformation. The Plant Journal. 35:219-236.

[39] C. Coffman, R.W. Doerge, M. Wayne, and L.M. McIntyre. 2003. Intersection tests for Single marker QTL analysis can be more powerful than two marker QTL analysis. BioMed Central (BMC) Genetics. 4:10.

[40] O. Abiola, J.M. Angel, P. Avner, A.A. Bachmanov, B. Bennett, E.P. Blankenhorn, D.A. Blizard, V. Bolivar, G.A. Brockmann, W.L. Casley, M. Cook, K.J. Buck, J.F. Bureau, E.J. Chesler, J.M. Cheverud, G.A. Churchill, J.C. Crabbe, W.E. Crusio, A.Darvasi, P. Demant, R.W. Doerge, R.W. Elliott, C.R. Farber, J. Flint, H. Gershenfeld, J.P. Gibson, W. Gu, G. de Haan, H. Himmelbauer, R. Hitzemann, K. Hunter, H.C. Hsu, F. Iraqi, R.C. Jansen, T.E. Johnson, G. Kempermann, F. Lammert, L. Lu, K.F. Manly, D.B. Matthews, J.F. Medrano, M. Mehrabian, G. Mittleman, B.A. Mock, J.S. Mogil, X. Montagutelli, G. Morahan, J.D. Mountz, H. Nagase, R.S. Nowakowski, B.F. O'Hara, A.V. Osadchuk, B. Paigen, A.A. Palmer, J.L. Peirce, D. Pomp, G.D. Rosen, M. Rosemann, L.C. Schalkwyk, Z. Seltzer, S. Settle, K. Shimomura, S. Shou, J.M. Sikela, L.D. Siracusa, J.L. Spearow, C. Teuscher, D.W. Threadgill, L.A. Toth, A.A. Toye, C. Vadasz, E. Wakeland, R.W. Williams, G. Van Zant, H.G. Zhang, F. Zou, and L. Flaherty. 2003. The nature and identification of quantitative trait loci: a community's view. Nature Genetics Reviews. 4:911-916.

[41] D. Cao*, B.A. Craig, and R.W. Doerge. 2003. Interval mapping for autopolyploids. Proceedings of Applied Statistics in Agriculture, Kansas State University. Edited by George Milliken, pp60-72.

[42] D. Cao*, T.C. Osborn, and R.W. Doerge. 2004. Correct estimation of preferential chromosome pairing in polyploids. Genome Research. 14:459-462.

[43] M. Bogdan, J.K. Ghosh, and R.W. Doerge. 2004. Modifying the Schwarz Bayesian Information Criterion to locate multiple interacting quantitative trait loci. Genetics. 167:989-999.

[44] H.-S. Lee, J. Wang, L. Tan, H. Jiang, M.A. Black*, A. Madlung, L. Lukens, J.C. Pires, L. Comai, T.C. Osborn, R.W. Doerge, and Z.J. Chen. 2004. Sensitivity of 70-mer oligonucleotides and cDNAs for microarray analysis of gene expression in Arabidopsis and its related species. Plant Biotechnology Journal. 2:45-57.

[45] Z.J. Chen, J. Wang, L. Tian, H.-S. Lee, J.J. Wang, M. Chen, J.J. Lee, C. Josefsson, A. Madlung, B. Watson, J.C. Pires, Z. Lippman, M. Vaughn, V. Colot, J.A. Birchler, R.W. Doerge, R.A. Martienssen, L. Comai, and T.C. Osborn. 2004. The development of an Arabidopsis model system for genome-wide analysis of polyploidy effects. Biological Journal of the Linnean Society. 82:689-700.

[46] Z. Lippman, A.-V. Gendrel, M. Black*, M. Vaughn, N. Dedhia, W.R. McCombie, K. Lavine, V. Mittal, B. May, K. Kasschau, J.C. Carrington, R.W. Doerge, V. Colot, and R. Martienssen 2004. Transposable elements mediate heterochromatin and epigenetic control. Nature. 430:471-476.

[47] K. Bradley, M.B. Boulware, H. Jiang*, R.W. Doerge, and R.L. Meisel. 2004. Sexual experience generates distinct patterns of gene expression in the nucleus accumbens and dorsal striatum of female syrian hamsters. Genes, Brain, and Behavior. 4(1):31-44.

[48] K. Kim*, M. West, R.W. Michelmore, D. St. Clair, and R.W. Doerge. 2004. Genetic mapping of gene expression levels: expression level polymorphism analysis for dissecting regulatory networks of plant disease resistance. The Proceedings of the Kansas State University Conference on Applied Statistics in Agriculture. Manhattan, KS. pp97-111.

[49] D. Cao*, B.A. Craig, and R.W. Doerge. 2004. Bayesian quantitative trait mapping of autopolyploids. The Proceedings of the Kansas State University Conference on Applied Statistics in Agriculture. Manhattan, KS.

[50] H. Jiang*, J. Wang, L. Tian, Z.J. Chen, and R.W. Doerge. 2004. Statistical analysis of 70-mer oligonucleotide microarray from polyploid experiments using repeated dye-swaps. The Proceedings of the Kansas State University Conference on Applied Statistics in Agriculture. Manhattan, KS.

[51] The Complex Traits Consortium (see publication 40 for list of members). 2004. The collaborative cross: A community resource for the genetic analysis of complex traits. Nature Genetics. 36(11):1133-7.

[52] J. Wang, J.J. Lee, H.-S. Lee, L. Tian, M. Chen, S. Rao, E.N. Wei, R.W. Doerge, L. Comai, and Z.J. Chen. 2005. Methods for genome-wide analysis of gene expression changes in polyploids. Methods in Enzymology. 395:570-96.

[53] L. Tian, M.P. Fong, J.J. Wang, N.E. Wei, H. Jiang*, R.W. Doerge, and Z.J. Chen. 2005. Reversible histone acetylation and deacetylation mediate genome-wide, promoter-dependent, and locus-speci c changes in gene expression during plant development. Genetics. 169:337-345.

[54] A. Madlung, A.P. Tyagi, B. Watson, H. Jiang*, T. Kagochi, R.W. Doerge, R. Martienssen, and L. Comai. 2005. Genomic changes in synthetic Arabidopsis polyploids. Plant Journal. 41(2):221-230.

[55] D. Cao*, B. Craig, and R.W. Doerge. 2005. A model selection based interval mapping method for autopolyploids. Genetics. 169:2371-2382.

[56] M. Bogdan and R.W. Doerge. 2005. Biased estimators of genetic effects and heritability in interval mapping. Heredity. 95:476-484.

[57] C. Coffman, R.W. Doerge, K.L. Simonsen, K. Nichols, C. Duarte, R. Wol nger, and L.M. McIntyre. 2005. Model selection in binary trait locus mapping. Genetics. 170:1281-1297.

[58] J. Stevens* and R.W. Doerge. 2005. Combining Affymetrix microarray results. BMC Bioinformatics. 6:57.

[59] J. Stevens* and R.W. Doerge. 2005. Meta-Analysis combines Affymetrix microarray results across laboratories. Comparative and Functional Genomics. 6:116-122.

[60] R.A. Martienssen, R.W. Doerge, and V. Colot. 2005. Epigenomic mapping in Arabidopsis using tiling microarrays. Chromosome Research. 13 3:299-308.

[61] B. Munneke*, K.A. Schlauch, K. Simonsen, W. Beavis, and R.W. Doerge. 2005. Adding con dence to gene expression clustering. Genetics. 170:2003-2011.

[62] J. Stevens* and R.W. Doerge. 2005. A Bayesian and covariate approach to combine results from multiple microarray studies. The Proceedings of the Kansas State University Conference on Applied Statistics in Agriculture. Manhattan, KS. pp133-147.

[63] K. Kim*, M. West, R.W. Michelmore, D. St. Clair, and R.W. Doerge. 2005. Old methods for new ideas: using gene expression levels to molecularly dissect complex traits. The Proceedings of the Stadler Genetics Symposium. March 2003. Edited by Perry Gustafson, Randy Shoemaker, and John Snape. Springer, NY. pp89-106.

[64] J. Wang, L. Tian, H-S Lee, N.E. Wei, H. Jiang*, B. Watson, A. Madlung, T.C. Osborn, R.W. Doerge, L. Comai, and Z.J. Chen. 2006. Genome-wide non-additive gene regulation in Arabidopsis allotetraploids. Genetics. 172:507-517.

[65] D.J. Kliebenstein, M.A.L. West, H. van Leeuwen, K. Kim*, R.W. Doerge, R.W. Michel-

more, and D.A. St. Clair. 2006. Genomic survey of gene expression diversity in Arabidopsis thaliana. Genetics. 172:1179-1189.

[66] C. Teuscher, R.W. Doerge, P.D. Fillmore, and E.P. Blankenhorn. 2006. eae36, A locus on mouse chromosome 4 controls susceptibiltiy to experimental allergic encephalomyelitis in older mice and mice immunized in the winter. Genetics. 172:1147-1153.

[67] M.A.L. West, H. van Leeuwen, A. Kozik, D.J. Kliebenstein, R.W. Doerge, D.A. St. Clair, and R.W. Michelmore. 2006. High-density haplotyping with microarray-based expression and single feature polymorphism markers in Arabidopsis. Genome Research. 16:787-795.

[68] D.J. Kliebenstein, M.A.L. West, H. van Leeuwen, O. Loudet, R.W. Doerge, and D.A. St. Clair. 2006. Identi cation of QTLs controlling gene expression networks de ned a priori. BMC Bioinformatics. 7(1):308.

[69] L. An*, N. Riddle, J. Birchler, and R.W. Doerge. 2006. Clustering a series of replicated polyploid gene expression experiments. The Proceedings of the Kansas State University Conference on Applied Statistics in Agriculture. Manhattan, KS. pp52-66.

[70] H. Jiang* and R.W. Doerge. 2006. A two-step multiple comparison procedure for a large number of tests and multiple treatments. Statistical Applications in Genetics and Molecular Biology. 5: 1, Article 28.

[71] J. M. Ordway, J.A. Bedell, R.W. Citek, A. Nunberg, A. Garrido, R. Kendall*, J.R. Stevens*, D. Cao*, R.W. Doerge, Y. Korshunova, H. Holemon, J.D. McPherson, N. Lakey, J. Leon, R.A. Martienssen, and J.A. Jeddeloh. 2006. Comprehensive DNA methylation pro ling in a human cancer genome identi es novel epigenetic targets. Carcinogenesis. 27(12):2409-2423.

[72] M.A.L. West, K. Kim*, D.J. Kliebenstein, H. van Leeuwen, R.W. Michelmore, R.W. Doerge, and D.A. St. Clair. 2007. Global eQTL mapping reveals the complex genetic architecture of transcript level variation in Arabidopsis. Genetics. 175:1441-1450.

[73] M. Vaughn, M. Tanurdzic, Z. Lippman, H. Jiang, R. Carrasquillo, V. Colot, R.W. Doerge and R.A. Martienssen. 2007. Epigenetic natural variation in Arabidopsis thaliana. Public Library of Science (PLoS) Biology. 5(7): e174.

[74] H. van Leeuwen, D.J. Kliebenstein, M.A.L. West, K. Kim*, R. van Poecke, F. Katagiri, R.W. Michelmore, R.W. Doerge, and D.A. St. Clair. 2007. Natural variation among Arabidopsis thaliana accessions for transcriptome response to exogenous salicylic acid. The Plant Cell. 19(7):2099-2110.

[75] J. Zhao, J. Wang, L. An*, R.W. Doerge, Z.J. Chen, C. Grau, J. Meng, and T. Osborn. 2007. Analysis of gene expression pro les in response to Sclerotinia sclerotiorum in Brassica napus. Planta. 227(1):13-24.

[76] J.M. Ordway, M.A. Budiman, Y. Korshunova, R.K. Maloney, J.A. Bedell, R.W. Citek, B. Bacher, S. Peterson, T. Rohl ng, J. Hall, R. Brown, N. Lakey, R.W. Doerge, R.A. Martienssen, J. Leon, J.D. McPherson, and J.A. Jeddeloh. 2007. Identi cation of novel high-frequency DNA methylation changes in breast cancer. Public Library of Science (PLoS) ONE. 12:1314.

[77] R.W. Doerge. 2007. Proper experimental design and sound statistical inference win every time: a commentary on 'Statistical design and the analysis of gene expression microarray data' by M. Kathleen Kerr and Gary A. Churchill. Genetics Research. 89(5-6): 505-507.

[78] H.-T. Leung, L. An*, J. Tseng-Crank, E. Kim, E.L. Harness, Y. Zhou, J. Kitamoto, G. Li, R.W. Doerge, and W.L. Pak. 2008. Phototransduction in Drosophila: Use of microarrays in cloning genes identi ed by chemically induced mutations causing ERG defects. In S.J. Fliesler and O.G. Kisselev (eds.), Signal Transduction in the Retina, Taylor and Francis/CRC Press, pp195-217.

[79] M. Bogdan, P. Biecek, R. Cheng*, F. Frommlet, J.K. Ghosh, and R.W. Doerge. 2008. Extending the modi ed Bayesian Information Criterion (mBIC) to dense markers and multiple interval mapping. Biometrics. 64(4):1162-1169.

[80] A.A. Long, E. Kim, H.-T. Leung, E. Woodruff III, L. An*, R.W. Doerge, W.L. Pak, and K. Broadie. 2008. Presynaptic calcium channel localization and calcium-dependent synaptic vesicle exocytosis regulated by the fuseless protien. Journal of Neuroscience. 28:3668 - 3682.

[81] G.A. Churchill and R.W. Doerge. 2008. Naive application of permutation testing leads to in ated type I error rates. Genetics. 178:609-610.

[82] H. Jiang* and R.W. Doerge. 2008. Estimating the proportion of true null hypotheses for multiple comparisons. Cancer Informatics. 4:25-32.

[83] H.-T. Leung, J. Tseng-Crank, E. Kim, C. Mahapatra, S. Shino, Y. Zhou, L. An, R.W. Doerge and W.L. Pak. 2008. DAG lipase activity is necessary for TRP channel regulation in Drosophila photoreceptors. Neuron. 58(6):884-896.

[84] M. Tanurdzic, M. Vaughn, H. Jiang*, L. Lee, E. Thompson, R.W. Doerge, and R.A. Martienssen. 2008. Epigenomic consequences of immortalized plant cell suspension culture. Public Library of Science Biology (PLoS Biology). 6(12):2880-2895.

[85] S.-Y. Yoo* and R.W. Doerge. Integrating Epigenomics Results. 2008. Epigenomics. A. Ferguson-Smith et al. (eds) Springer-Verlag. 37-52.

[86] R.W. Doerge. 2008. Statistical Advances in Functional Genomics. R. Varshney and R. Tuberosa (eds.), Genomic Assisted Crop Improvement: Vol 1: Genomics Approaches and Platforms, 315-332. Springer-Verlag.

[87] K. Spach, L. An, M. Blake, E. Blankenhorn, J. Bunn, R. Doerge, B. McElvany, R. Noubade, K. Tung, and C. Teuscher. 2008. Age, season and stress in uence EAE sexual dimorphism in SJL/J mice. Journal of Neuroimmunology. 203(2):212-212.

[88] P. Jones, T. Archer, S. Baylin, et al. 2008. Moving AHEAD with an international human epigenome project . Nature. 454(7205):711-715.

[89] L. An* and R.W. Doerge. 2008. Dynamic clustering of cell-cycle gene expression data. The Proceedings of the Kansas State University Conference on Applied Statistics in Agriculture. Manhattan, KS. pp18-36.

[90] S.-Y. Yoo* and R.W. Doerge. 2008. A two-stage approach for estimating the effect of DNA methylation on differential expression using tiling array technology. 2008. The Proceedings of the Kansas State University Conference on Applied Statistics in Agriculture. Manhattan, KS. pp124-137.

[91] R.T. Gaeta, S.-Y. Yoo*, J.C. Pires, R.W. Doerge, Z.J. Chen, and T.C. Osborn. 2009. Analysis of gene expression in resynthesized Brassica napus allopolyploids using Arabidopsis 70mer oligo microarrays. Public Library of Science (PLoS) ONE 4(3): e4760. doi:10.1371/journal.pone.0004760.

[92] M. Bremer* and R.W. Doerge. 2009. The KM-Algorithm identi es genes in time series gene expression data. Advances in Bioinformatics. Volume 2009, Article ID 284251, 10 pages, doi:10.1155/2009/284251.

[93] N. C. Riddle, H. Jiang*, L. An*, R.W. Doerge, and J.A. Birchler. 2009. Gene expression analysis at the intersection of ploidy and hybridity in maize. Theoretical and Applied Genetics. 120(2):341-353.

[94] R.W. Doerge and K. Kim*. 2009. Statistical challenges in modeling expression quantitative traits. Proceedings of the 24th International Workshop on Statistical Modelling. James E. Booth, Editor, pp13-22.

[95] G.R. Olbricht*, N. Sardesai, S.B. Gelvin, B.A. Craig, and R.W. Doerge. 2009. Statistical methods for Affymetrix tiling array data. The Proceedings of the Kansas State University Conference on Applied Statistics in Agriculture. Manhattan, KS. pp111-125.

[96] P. L. Auer* and R.W. Doerge. 2009. Statistical issues in next generation sequencing. The Proceedings of the Kansas State University Conference on Applied Statistics in Agriculture. Manhattan, KS. pp69-84.

[97] A. Lipka*, G. McCabe and R.W. Doerge. 2009. Associating SNPs with binary traits. The Proceedings of the Kansas State University Conference on Applied Statistics in Agriculture. Manhattan, KS. pp5-19.

[98] C. Ochsenfeld*, K. Jennings, and R.W. Doerge. 2009. Mapping QTL with covariates. The Proceedings of the Kansas State University Conference on Applied Statistics in Agriculture. Manhattan, KS. pp126-140.

[99] D. Pignatta, B.P. Dilkes, S.Y. Yoo*, I.M. Henry, A. Madlung, R.W. Doerge, Z. J. Chen, L. Comai. 2010. Differential sensitivity of the Arabidopsis thaliana transcriptome and enhancers to the effects of genome doubling. New Phytologist. 186(1):194-206.

[100] A. Rau*, F. Jaffrezic, J.-L. Foulley, and R.W. Doerge. 2010. An empirical Bayesian method for estimating biological networks from temporal microarray data. Statistical Applications in Molecular Biology and Genetics. 9(1) Article 9.

[101] M. Bremer* and R.W. Doerge. 2010. Statistics at the Bench: A Step-by-Step Handbook for Biologists. Cold Spring Harbor Press. Cold Spring Harbor, NY.

[102] P.L. Auer* and R.W. Doerge. 2010. Statistical design and analysis of RNA sequencing data. Genetics. 185: 405-416.

[103] A.A. Long, C. Mahapatra, H.-T. Leung, E.A. Woodruff III, J. Rohrbough, L. An*, R.W. Doerge, M.M. Metzstein, S. Shino, W.L. Pak, and K. Broadie. 2010. The nonsense-mediated decay pathway is critical for maintaining synapse architecture and synaptic vesicle cycle efficacy. Journal of Cell Science. 3303-3315.

[104] L. Yu* and R.W. Doerge. 2010. A semi-non-parametric mixture model for selecting functionally consistent proteins. BMC Bioinformatics. 11:486 doi:10.1186/1471-2105-11-486.

[105] P.L. Auer* and R.W. Doerge. 2010. Functional divergence of duplicated genes in the soybean genome. The Proceedings of the Kansas State University Conference on Applied Statistics in Agriculture. Manhattan, KS. pp171-185.

[106] A. Rau*, F. Jaffrezic, J.-L. Foulley, and R.W. Doerge. 2010. Approximate Bayesian approaches for reverse engineering biological networks. The Proceedings of the Kansas State University Conference on Applied Statistics in Agriculture. Manhattan, KS. pp202-216.

[107] G. Olbricht*, B.A. Craig, and R.W. Doerge. 2010. Modeling DNA methylation tiling array data. The Proceedings of the Kansas State University Conference on Applied Statistics in Agriculture. Manhattan, KS. pp63-84.

[108] S. Srivastava* and R.W. Doerge. 2010. A non-parametric empirical Bayes approach for estimating transcript abundance in unreplicated next-generation sequencing data. The Proceedings of the Kansas State University Conference on Applied Statistics in Agriculture. Manhattan, KS. pp230-244.

[109] T. Achberger*, J.C. Fleet, D.E. Salt, and R.W. Doerge. 2010. Introduction to selecting subsets of traits for quantitative trait loci analysis. The Proceedings of the Kansas State University Conference on Applied Statistics in Agriculture. Manhattan, KS. pp267-286.

[110] P.L. Auer* and R.W. Doerge. 2011. A two-stage Poisson model for testing RNA-seq data. Statistical Applications in Genetics and Molecular Biology. 10(1) Article 26.

[111] D. Baumann* and R.W. Doerge. 2011. Issues in testing DNA methylation using next-generation sequencing. The Proceedings of the Kansas State University Conference on Applied Statistics in Agriculture. Manhattan, KS. pp1-14.

[112] S. Srivastava* and R.W. Doerge. 2011. A hierarchical Bayesian approach for detecting differential gene expression in unreplicated RNA-sequencing data. The Proceedings of the Kansas State University Conference on Applied Statistics in Agriculture. Manhattan, KS. pp166-189.

[113] P.L. Auer*, S. Srivastava*, and R.W. Doerge. 2012. Differential Expression: The next generation and beyond. Brie ngs in Functional Genomics. 11(1):57-62.

[114] S. Srivastava* and R.W. Doerge. 2012. Purdue Statistics: A journey through time. "Strength in Numbers: The Rising of Academic Statistics Departments in the United States". Editors Alan Agresti and Xiao-Li Meng. Springer. pp229-242.

[115] G. Olbricht*, B. Craig, and R.W. Doerge. 2012. Incorporating genomic annotation into a hidden markov model for DNA methylation tiling array data. Statistical Applications in Genetics and Molecular Biology. 11(5) DOI: 10.1515/1544-6115.1775.

[116] A. Rau*, F. Jaffrezic, J.-L. Foulley and R. W. Doerge. 2012. Reverse engineering gene regulatory networks using approximate Bayesian computation. Statistics and Computing: 22(6):1257-127.

[117] L. An* and R.W. Doerge. 2012. Dynamic clustering of gene expression. ISRN Bioinformatics, doi:10.5402/2012/537217.

[118] A.A. Elias*, K.R. Robbins, D. Niyogi, J.J. Camberato, R.W. Doerge, and M.R. Tuinstra. 2012. Evaluation of genotype by environment interactions from unreplicated multi-environmental trials of hybrid maize. The Proceedings of the Kansas State University Conference on Applied Statistics in Agriculture. Manhattan, KS. pp1-12.

[119] D. Baumann* and R.W. Doerge. 2012. Correcting for amplification bias in next-generation sequencing data. The Proceedings of the Kansas State University Conference on Applied Statistics in Agriculture. Manhattan, KS. pp36-49.

[120] X. Chen* and R.W. Doerge. 2012. Towards better FDR procedures for discrete test statistics. The Proceedings of the Kansas State University Conference on Applied Statistics in Agriculture. Manhattan, KS. pp294-303.

[121] S. Srivastava* and R.W. Doerge. 2012. The nuances of statistically analyzing next-generation sequencing data. The Proceedings of the Kansas State University Conference on Applied Statistics in Agriculture. Manhattan, KS. pp233-267.

[122] A. Roulin, P.L. Auer*, M. Libault, J. Schlueter, A. Farmer, G. May, G. Stacey, R.W. Doerge and S.A. Jackson. 2013. The fate of duplicated genes in a polyploid plant genome. The Plant Journal. 73:143153.

[123] C.N. Billingsley, J.A. Allen, J.D. Blazek, D.D. Baumann*, A. Newbauer, A. Darrah, M. Clement, R.W. Doerge, and R.J. Roper. 2013. Non-trisomic homeobox gene expression during craniofacial development in Down syndrome mice. American Journal of Medical Genetics. 161(8):1866-1874.

[124] R. Cheng*, J. Borevitz, and R.W. Doerge. 2013. Selecting informative traits for multivariate quantitative trait locus mapping helps to gain optimal power. Genetics. 195(3):683-691.

[125] N. Sardesai, H. Chen, H. Yi, G.R. Olbricht*, K. Laluk, R.W. Doerge, T. Mengiste, and S.B. Gelvin. Cytokinins secreted by agrobacterium promote transformation by repressing a plant Myb transcription factor. Science Signaling 6 (302):ra100.

[126] D.D. Baumann and R.W. Doerge. 2014. Robust adjustment of sequence tag abundance. Bioinformatics. 30(5):601-605.

[127] I. Pardo, H.A. Lillemoe, R.J. Blosser, M. Choi, C.A.M. Sauder, D.K. Doxey, T. Mathieson, B.A. Hancock, D. Baptiste, R. Atale, M. Hickenbotham, J. Zhu, J. Glasscock, A.M.V. Storniolo, F. Zheng, R.W. Doerge, Y. Liu, S. Badve, M. Radovich, and S.E. Clare. 2014. Next-generation transcriptome sequencing of the premenopausal breast epithelium using specimens from a normal human breast tissue bank. Breast Cancer Research. 16(2):R26

[128] F. Lin, M. Zhao, D.D. Baumann, J. Ping, L. Sun, Y. Liu, B. Zhang, Z. Tang, E. Hughes, R.W. Doerge, T.J. Hughes and J. Ma. 2014. Molecular response to the pathogen phytophthora sojae among ten soybean near isogenic lines revealed by comparative transcriptomics. BMC Genomics. 15(1):18

[129] D.D. Baumann and R.W. Doerge. 2014. MAGI: Methylation analysis using genome information. Epigenetics. 9(5):0-1.

[130] M. Bremer* and R.W. Doerge. 2015. Using R at the Bench: Step-by-Step Analytics for Biologists. Cold Spring Harbor Press. Cold Spring Harbor, NY.

Published Abstracts, Non-Refereed Publications, and Conference Proceedings (43)

Current and Purdue graduate students denoted by an asterisk (*).

[1] R.W. Doerge. 1988. Information of Fixed Cluster Samples for Genetic Traits Involving Mixtures of Distributions. Master of Statistics in Mathematics, University of Utah.

[2] M.M. Shoukri, R.H. Ward, R.W. Doerge. 1989. Statistical inference from the genetic mixture of normal distributions, Proceedings of the 47th Session of the International Statistical Institute.

[3] R.D. Sederoff, D. Grattapaglia, P. Wilcox, J. Chaparro, D. O'Malley, S. McCord, R. Whetten, L. McIntyre, B. Weir, R.W. Doerge, F. Bridgewater, S. Thorpe. 1992. Use of PCR-based RAPD markers for genetic mapping in conifers. Abstracts of papers of the American Chemical Society. 203: 73-BTEC, Part 3.

[4] B.S. Weir and R.W. Doerge. 1992. Statistical issues in the search for QTLs. XVI International Biometric Conference Proceedings, Contributed Papers p. 164.

[5] B.S. Weir and R.W. Doerge. 1993. Biometrical issues in the search for genes affecting quantitative traits. American Statistical Association Annual Meeting Abstracts p311.

[6] R.W. Doerge. 1993. Statistical Methods for Locating Quantitative Trait Loci with Molecular Markers. Ph.D. Dissertation. Department of Statistics. North Carolina State University, Raleigh, NC.

[7] G.A. Churchill and R.W. Doerge. 1994. Mapping quantitative trait loci in experimental populations. Proceedings of the Biometric Conference. Ontario, Canada.

[8] R.W. Doerge and G.A. Churchill. 1994. Analysis of molecular marker data. Issues in genetic mapping of quantitative trait loci. Proceedings of the ASHA/CSSA 2nd Joint Plant Breeding Symposium. Corvallis, Oregon.

[9] R.W. Doerge, Z-B. Zeng and B.S. Weir. 1994. Statistical issues in the search for genes affecting quantitative traits in populations. Proceedings of the ASHA/CSSA 2nd Joint Plant Breeding Symposium. Corvallis, Oregon.

[10] R.W. Doerge. 1996. Locating genes in plants, animals and humans using Statistics and Genetics. Sequel. Purdue University School of Science publication.

[11] R.W. Doerge. 1998. Characterizing germplasm collections using molecular markers. Abstracts Proceedings of the American Statistical Association.

[12] R.W. Doerge. 1999. Risk communication for locating quantitative trait loci (QTL) in experimental populations. Abstracts Proceedings of the American Statistical Association.

[13] S.M. Brouder, C.H. Nakatsu and R.W. Doerge. 1999. Microbial community dynamics in the rhizosphere of Zea mays L. and Glycine max. Amer. Soc. Agronomy, Salt Lake City, UT (Oct. 31 - Nov. 5, 1999).

[14] C.H. Nakatsu, S.M. Brouder, F. Wanjau, J.D. Wilbur*, and R.W. Doerge. 2000. Impact of tillage and crop rotation on corn development and its associated microbial community. Proceedings of the 15th Conference of the International Soil Tillage Research Organization (ISTRO). July 2-7, 2000. Fort Worth, TX (CD-ROM).

[15] J.D. Wilbur*, S.M. Brouder, C.H. Nakatsu, and R.W. Doerge. 2000. Statistical analysis of rhizosphere microbial communities. In Proceedings of Interface 2000. The 32nd Symposium on the Interface: Computing science and statistics. New Orleans, LA (CD-ROM).

[16] F.M Wanjau, S.M Brouder, C.H. Nakatsu, and R.W. Doerge. 2000. Influence of crop rotation and tillage practices on root architecture of corn and soybean. American Society of Agronomy Abstracts. Minneapolis, MN.

[17] R.J. Roper, R.W. Doerge, K.S.K. Tung, C. Teuscher. 2000. Genetic loci controlling thymectomy-induced autoimmune ovarian dysgenesis. NIH Workshop on The Ovary, Gensis, Function and Failure (Bethesda, MD).

[18] M.A. Black*, B.A. Craig, M.J. Tanurdzic*, and R.W. Doerge. 2001. A Bayesian approach to the analysis of cDNA microarray data. Proceedings of the 33rd Symposium on the Interface.

[19] D.A. Bulinski*, C.H. Nakatsu, J.D. Wilbur*, S. M. Brouder, and R.W. Doerge. 2001. Rhizosphere Microbial population dynamics over three eld seasons. American Society of Agronomy Abstracts. Charlotte, NC.

[20] H.-S. Lee, J. Wang, L. Tian, L. Lukens, A. Madlung, M.A. Black*, L. Comai and R.W. Doerge. 2002. Genome-wide expression analysis of orthologous genes in Arabidopsis and Brassica polyploids. Plant Biology 2002. Denver, CO.

[21] T.C. Osborn, L. Lukens, J.C. Pires, Z.J. Chen, L. Comai, R.W. Doerge, R.A. Martienssen. 2002. Why become a polyploid? Plant and Animal Genome X, p65.

[22] T.C. Osborn, L. Lukens, J.C. Pires, M.E. Schranz, H.-S. Lee, Z.J. Chen, R.W. Doerge. 2002. Gene expression studies in Brassica. 13th Crucifer Genet Workshop Abstracts, p71.

[23] M.A. Black*, B.A. Craig, J. Deely, R.W. Doerge. 2002. Bayesian analysis of cDNA microarray data. Joint Statistical Meetings, p271.

[24] J.D. Wilbur*, J.K. Ghosh, C.H. Nakatsu, S.M. Brouder, R.W. Doerge. 2002. An application of empirical bayes model selection to microbial community ngerprint analysis. Joint Statistical Meetings, p272.

[25] A. Madlung, B. Watson, R. Masuelli, Z. Lippman, V. Colot, R. Martienssen, R.W. Doerge, M. Black, L. Comai, L. 2003. Genetic and epigenetic changes in synthetic allopolyploids of Arabidopsis thaliana. Plant and Animal Genome XI, p63.

[26] D. Cao*, B.A. Craig, R.W. Doerge. 2003. A maximum likelihood-based interval mapping model for autopolyploids. Joint Statistical Meetings, p27.

[27] K. Kim and R.W. Doerge. 2003. Statistical issues in dissecting regulatory networks associated with complex traits: genetic mapping of gene expression levels. Joint Statistical Meetings, p27.

[28] B.A. Craig and R.W. Doerge. 2003. Gene expression data: The technology and statistical analysis. Joint Statistical Meetings, p67.

[29] A. Madlung, B. Watson, H. Jiang*, T. Kagochi, R.W. Doerge, L. Comai, R. Martienssen. 2004. Transposon activation in Arabidopsis neopolyploids. Arabidopsis Meeting, Berlin, Germany.

[30] J. Chen, J. Wang, L. Tian, E. Weil, M. Chen, S. Rao, R.W. Doerge, H. Jiang*, L. Comai, B. Watson. 2005. Transcriptome divergence and mechanisms of non-additive gene regulation in Arabidopsis allopolyploids. International Botanical Congress.

[31] M. Bogdan, J. K. Ghosh, R.W. Doerge, P. Biecek, A. Baierl, A. Futschik, F. Frommlet. 2005. Modi ed version of Schwarz Bayesian Information Criterion for localization of multiple interacting quantitative trait loci. Paris, France. Annals of Human Genetics.

[32] M. Bogdan, J.K. Ghosh, R.W. Doerge, P. Biecek, A. Baierl, A. Futschik, F. Frommlet. 2005. Modi ed version of Bayesian Information criterion for localization of multiple interacting quantitative trait loci. Ann. Hum. Gen. 69:765.

[33] M. Vaughn, M. Tanurdzic, Z. Lippman, H. Jiang*, V. Colot, R.W. Doerge, and R. Martienssen. 2005. Epigenomic pro ling of Arabidopsis Thaliana. Cold Spring Harbor Laboratory Genome Informatics Meeting. Cold Spring Harbor, NY.

[34] R.A. Martienssen, M. Zaratiegui, D. Irvine, D. Goto, K. Slotkin, M. Tanurdzic, Z. Lippman, M. Vaughn, B. May, Z. Cande, V. Colot, and R.W. Doerge. 2007. Silent running: RNA interference and heterochromatic modi cation. Chromosome Research 15:20-21 Supplement 2.

[35] R.A. Martienssen, M. Tanurdzic, K. Slotkin, P. Finigan, K. Creasey, P. Auer*, M.Vaughn, J.-P. Vielle-Calzada, and R.W. Doerge. 2011. Heterochromatin reprogramming by small RNA regulates germ cell fate in Arabidopsis. Plant Epigenome Workshop. Plant and Animal Genome Conference. San Diego, CA.

[36] J.M. Cardenas-Mora, A. Schafer, C. Plachot, J. Stanley, D. Stegelman, A. Lipka, D. Baumann*, K. Hodges, K. McDole, L. An*, R.W. Doerge, and S.A. Lelievre. 2011. CDS1, a potential novel marker of breast cancer development. 3rd Annual National Predoctoral Clinical Research Training Program Meeting. St Louis, MO.

[37] S. Chudalyandi, R.W. Doerge, S. Srivastava*, and J. Birchler. 2011. Gene expression profiling in normal and interploidy endosperms of maize. ASPB Plant Biology Meeting.

[38] M. Tanurdzi, P. Auer*, P. Finigan, E. Ernst, B. Dilkes, L. Comai, B.C. Meyers, M.W. Vaughn, R.W. Doerge, R.A. Martienssen. 2011. Small RNA mediate transposon instability in plant inter-speci c hybrids in a parent-speci c manner. European Science Foundation (ESF) European Molecular Biology Organization (EMBO) "Epigenetics in Context: From Ecology to Evolution". Sant Feliu de Guixols, Spain.

[39] R.J. Roper, C. Billingsley, J. Allen, J. Blazek, D. Baumann, A, Newbauer, A. Darrah1, B.C. Long, B. Young, M. Clement, and R.W. Doerge. 2011. Non-trisomic homebox gene AND sox9 expression alters craniofacial development in a down syndrome mouse model. Mouse Genetics Conference. Washington, D.C.

[40] A.A. Elias, K.R. Robbins, Dev Niyogi, James J. Camberato, R.W. Doerge, and M.R. Tuinstra. 2011. Estimation and prediction of hybrid maize performance in mega-environments and changing climate American Society of Agronomy. San Antonio, TX.

[41] R.A. Martienssen, M. Tanurdzic, P. Baduel, J. Calarco, K. Creasey, F. vanEx, Y. Jacob, P.L. Auer, J.-P. Vielle-Calzada, and R.W Doerge. 2011. RNA interference, heterochromatin reprogramming and germ cell fate. Conference on epigenetics and the inheritance of acquired states. Boston, MA.

[42] R.A. Martienssen, M. Tanurdzic, P.L. Auer, P.E. van Ernst, B.P. Dilkes, L. Comai,B.C. Meyers, M. Vaughn, R.W. Doerge. 2012. Transposon activation in Arabidopsis allopolyploids is mediated by RNA interference. Plant and Animal Genome XX, San Diego, CA.

[43] R.W. Doerge. 2012. Statistical issues and the analysis of next-generation sequencing data. Plant and Animal Genome XX, San Diego, CA.