Quick Links: Publications, Papers Under Review, Papers in Preparation

Publications

• K. P. Lennox, D. B. Dahl, M. Vannucci, R. Day, J. W. Tsai (2009), A Dirichlet Process Mixture of Hidden Markov Models for Protein Structure Prediction, Annals of Applied Statistics, in press. Complete paper
• S. Kim, D. B. Dahl, M. Vannucci (2009), Spike and Slab Dirichlet Process Prior for Multiple Hypothesis Testing in Random Effects Models, Bayesian Analysis, 4, 413-444. Complete paper.
• L. Tao, D. B. Dahl, L. M. Perez, D. H. Russell (2009), The Contributions of Molecular Framework to IMS Collision Cross-sections of Gas-phase Peptide Ions, Journal of the American Society for Mass Spectrometry, 20, 1593-1602. Complete paper.
• D. B. Dahl (2009), Bayesian Methods for Protein Structure Prediction: Annoted Bibliography, ISBA Bulletin, 16, 6-8. Complete bulletin.
• K. P. Lennox, D. B. Dahl, M. Vannucci, J. W. Tsai (2009), Density Estimation for Protein Conformation Angles Using a Bivariate von Mises Distribution and Bayesian Nonparametrics, Journal of the American Statistical Association, 104, 586-596. Complete paper with correction and supplement.
• D. B. Dahl (2009), Modal Clustering in a Class of Product Partition Models, Bayesian Analysis, 4, 243-264. Complete paper. Software.
• D. B. Dahl, S. Crawford (2009), RinRuby: Accessing the R Interpreter from Pure Ruby, Journal of Statistical Software, 29(4), 1-18. Complete paper. Software and website.
• D. B. Dahl, Z. Bohannan, Q. Mo, M. Vannucci, J. W. Tsai (2008), Assessing Side-Chain Perturbations of the Protein Backbone: A Knowledge Based Classification of Residue Ramachandran Space, Journal of Molecular Biology, 378, 749-758. Personal version, Publisher's version.
• D. B. Dahl, Q. Mo, M. Vannucci (2008), Simultaneous Inference for Multiple Testing and Clustering via a Dirichlet Process Mixture Model, Statistical Modelling, 8, 23-39. Complete paper, slides of talk, video of talk (ogg/theora), video of talk (mpeg-4) (from Third Erich L. Lehmann Symposium).
• D. B. Dahl, M. A. Newton (2007), Multiple Hypothesis Testing by Clustering Treatment Effects, Journal of the American Statistical Association, 102, 517-526. Complete paper, see also the slides and video for paper above.
• D. B. Dahl (2007), Discussion of Jain and Neal's "Splitting and Merging Components of a Nonconjugate Dirichlet Process Mixture Model," Bayesian Analysis, 2, 473-478. Paper, discussion, and rejoinder.
• D. B. Dahl (2006), Model-Based Clustering for Expression Data via a Dirichlet Process Mixture Model, in Bayesian Inference for Gene Expression and Proteomics, Kim-Anh Do, Peter Müller, Marina Vannucci (Eds.), Cambridge University Press. Complete paper. Software implementing least-squares clustering.
• D. Kwon, S. Kim, D. B. Dahl, M. Swartz, M. Tadesse and M. Vannucci (2006), Identification of DNA Regulatory Motifs and Regulators by Integrating Gene Expression and Sequence Data, in Bayesian Inference for Gene Expression and Proteomics, Kim-Anh Do, Peter Müller, Marina Vannucci (Eds.), Cambridge University Press.
• S. Sengupta, J. A. den Boon, I.-H. Chen, M. A. Newton, D. B. Dahl, M. Chen, Y.-J. Cheng, W. H. Westra, C.-J. Chen, A. Hildesheim, B. Sugden, P. Ahlquist (2006), Genome-Wide Expression Profiling Reveals EBV-Associated Inhibition of MHC Class I Expression in Nasopharyngeal Carcinoma, Cancer Research, 66, 7999-8006.
• M. A. Croft, A. Glasser, G. Heatley, J. McDonald, T. Ebbert, D. B. Dahl, N. V. Nadkarni, P. L. Kaufman (2006), Accommodative Ciliary Body and Lens Function in Rhesus Monkeys, I: Normal Lens, Zonule and Ciliary Process Configuration in the Iridectomized Eye, Investigative Ophthalmology and Visual Science, 47, 1076-1086.
• J. A. Mattison, M. A. Croft, D. B. Dahl, G. S. Roth, M. A. Lane, D. K. Ingram, P. L. Kaufman (2005), Accommodative Function in Rhesus Monkeys: Effects of Aging and Calorie Restriction, Journal of the American Aging Association, 27, 59-67.
• S. Wamsley, B. T. Gabelt, D. B. Dahl, G. L. Case, R. W. Sherwood, C. A. May, M. R. Hernandez, P. L. Kaufman (2005), Vitreous Glutamate Concentration and Axon Loss in Monkeys with Experimental Glaucoma, Archives of Ophthalmology, 123, 64-70.
• N. Binkley, D. B. Dahl, T. Kawahara-Baccus, D. Krueger, R. J. Colman (2003), Bone Loss Assessment in Ovariectomized Rats Utilizing Two Dual-Energy X-Ray Absorptiometers, Journal of Bone and Mineral Research, 18, 370-375.
• N. T. Taylor, G. M. Burlingame, K. B. Kristensen, A. Fuhriman, J. Johansen, D. B. Dahl (2001), A Survey of Mental Health Care Provider's and Managed Care Organization Attitudes Toward, Familiarity with, and Use of Group Interventions, International Journal of Group Psychotherapy, 51(2), 243-263.
• M. Lopez, N. L. Van Zeeland, D. B. Dahl, R. Weindruch, J. M. Aiken (2000), Cellular Phenotypes of Age-Associated Skeletal Muscle Mitochondrial Abnormalities in Rhesus Monkeys, Mutation Research, 452, 123-138.

Papers Under Review

• D. B. Dahl, R. Day, J. W. Tsai (2009), Distance-Based Probability Distribution on Set Partitions with Applications to Protein Structure Prediction, Journal of the Royal Statistical Society: Series B, resubmitted.
• P. Sukhanov, K. P. Lennox, D. B. Dahl, M. Vannucci, R. Day, T. Ho, J. Tsai (2009), Protein Loop Modeling Using a Knowledge-based Density Estimation Method, PLoS Computational Biology, submitted.