# David B. Dahl

##
Associate Professor

Department of Statistics

Brigham Young University

Email: dahl@stat.byu.edu

Office: 208 TMCB

Phone: 801-422-9222

Fax: 801-422-0635

Department of Statistics

Brigham Young University

223 TMCB

Provo, UT 84602

## Biography

David B. Dahl is an Associate Professor in the Department of Statistics at Brigham Young University. He started his academic career at Texas A&M University as an Assistant Professor in 2004, was promoted with tenure in 2010, and moved to BYU in 2012. He did doctoral work at the University of Wisconsin -- Madison in the Department of Statistics and the Department of Biostatistics and Medical Informatics under the direction of Michael Newton, receiving his Ph.D. in 2004. He received B.S. and M.S. degrees from Brigham Young University in 1997 and 1998, working on his masters with Scott Grimshaw in the Department of Statistics. During 2007-2012, Dr. Dahl was an adjunct faculty member in the Division of Quantitative Sciences at the University of Texas, M.D. Anderson Cancer Center.

David B. Dahl's research interests are
Bayesian nonparametrics, model-based clustering, random partition models, protein structure prediction, bioinformatics, and statistical computing.
His work has appeared in journals including the
*Journal of the American Statistical Association*,
*Annals of Applied Statistics*, and
*Bayesian Analysis*. He teaches both undergraduate and
graduate classes, including Bayesian statistics, statistical methods, and statistical computing.

## Papers Under Review

**D. B. Dahl**, R. Day, J. Tsai (2014), Random Partition Distribution Indexed by Pairwise Information,, revise and resubmit.*Journal of the American Statistical Association***D. B. Dahl**, R. D. Payne, Deepthi Uppalapati (2014), jvmr: Integration of R, Java, and Scala,, revise and resubmit. Paper.*Journal of Statistical Software*

## Publications

- Q. Li,
**D. B. Dahl**, M. Vannucci, H. Joo, J. W. Tsai (2014), Bayesian Model of Protein Primary Sequence for Secondary Structure Prediction,, accepted. Paper.*PLOS ONE* - R. Day, H. Joo, A. Chavan, K. P. Lennox, Y. A. Chen,
**D. B. Dahl**, M. Vannucci, J. Tsai (2013), Understanding the General Packing Rearrangements Required for Successful Template Based Modeling of Protein Structure from a CASP Experiment,, 42, 40-48. Paper.*Computational Biology and Chemistry* - S. Schwartz, I. Friedberg, I. V. Ivanov, L. A. Davidson, J. S. Goldsby,
**D. B. Dahl**, D. Herman, M. Wang, S. M. Donovan, R. S. Chapkin (2012), A Metagenomic Study of Diet-Dependent Interaction Between Gut Microbiota and Host in Infants Reveals Differences in Immune Response,, 2012, 13:r32. Paper.*Genome Biology* - A. G. Chavan, H. Joo, R. Day, K. P. Lennox, P. Sukhanov,
**D. B. Dahl**, M. Vannucci, and J. W. Tsai (2011), Near-Native Protein Loop Modeling using Nonparametric Density Estimation Accommodating Sparcity., 7(10): e1002234. Paper.*PLoS Computational Biology* - R. Day, K. P. Lennox,
**D. B. Dahl**, M. Vannucci, and J. W. Tsai (2010), Characterizing the regularity of tetrahedral packing motifs in protein tertiary structure., 26, 3059-3066. Paper.*Bioinformatics* - K. P. Lennox,
**D. B. Dahl**, M. Vannucci, R. Day, J. W. Tsai (2010), A Dirichlet Process Mixture of Hidden Markov Models for Protein Structure Prediction,, 4, 916-962. Paper. Publisher's Link. Software.*Annals of Applied Statistics* - S. Kim,
**D. B. Dahl**, M. Vannucci (2009), Spike and Slab Dirichlet Process Prior for Multiple Hypothesis Testing in Random Effects Models,, 4, 707-732. Paper.*Bayesian Analysis* - 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,, 20, 1593-1602. Paper.*Journal of the American Society for Mass Spectrometry* **D. B. Dahl**(2009), Bayesian Methods for Protein Structure Prediction: Annoted Bibliography,, 16(2), 6-8. Bulletin.*ISBA 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,, 104, 586-596. Paper with correction and supplement.*Journal of the American Statistical Association* **D. B. Dahl**(2009), Modal Clustering in a Class of Product Partition Models,, 4, 243-264. Paper. Software.*Bayesian Analysis***D. B. Dahl**, S. Crawford (2009), RinRuby: Accessing the R Interpreter from Pure Ruby,, 29(4), 1-18. Paper. Software and website.*Journal of Statistical Software***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,, 378, 749-758. Personal version, Publisher's version.*Journal of Molecular Biology***D. B. Dahl**, Q. Mo, M. Vannucci (2008), Simultaneous Inference for Multiple Testing and Clustering via a Dirichlet Process Mixture Model,, 8, 23-39. Paper, slides of talk, video of talk (ogg/theora), video of talk (mpeg-4) (from Third Erich L. Lehmann Symposium).*Statistical Modelling***D. B. Dahl**, M. A. Newton (2007), Multiple Hypothesis Testing by Clustering Treatment Effects,, 102, 517-526. Paper, see also the slides and video for paper above.*Journal of the American Statistical Association***D. B. Dahl**(2007), Discussion of Jain and Neal's "Splitting and Merging Components of a Nonconjugate Dirichlet Process Mixture Model,", 2, 473-478. Paper, discussion, and rejoinder.*Bayesian Analysis***D. B. Dahl**(2006), Model-Based Clustering for Expression Data via a Dirichlet Process Mixture Model, in, Kim-Anh Do, Peter Müller, Marina Vannucci (Eds.), Cambridge University Press. Paper. Software implementing least-squares clustering.*Bayesian Inference for Gene Expression and Proteomics*- 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, Kim-Anh Do, Peter Müller, Marina Vannucci (Eds.), Cambridge University Press.*Bayesian Inference for Gene Expression and Proteomics* - 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,, 66, 7999-8006.*Cancer Research* - 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,, 47, 1076-1086.*Investigative Ophthalmology and Visual Science* - 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,, 27, 59-67.*Journal of the American Aging Association* - 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,, 123, 64-70.*Archives of Ophthalmology* - 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,, 18, 370-375.*Journal of Bone and Mineral Research* - 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,, 51(2), 243-263.*International Journal of Group Psychotherapy* - 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,, 452, 123-138.*Mutation Research*

## Teaching at Brigham Young University (last semester taught)

- STAT 121: Principles of Statistics (Fall 2012)
- STAT 123: Introduction to R Programming (Fall 2014)
- STAT 223: Applied R Programming (Fall 2014)
- STAT 340: Inference (Fall 2013)
- STAT 624: Statistical Computation (Fall 2014)

## Teaching at Texas A&M University (last semester taught)

- STAT 302: Statistical Methods (Spring 2012)
- STAT 604: Introduction to Statistical Computing (Spring 2007)
- STAT 605: Advanced Statistical Computations (Spring 2010)
- STAT 651: Statistics in Research I (Fall 2008)
- STAT 689: Introduction to Applied Bayesian Methods (Fall 2011)

## Software

bamboo | Software implementation of the methods described in: Q. Li, D. B. Dahl, M. Vannucci, H. Joo, J. W. Tsai (2014), Bayesian Model of Protein Primary Sequence for Secondary Structure Prediction, , accepted. Paper.PLOS ONE | |

jvmr | Software described in: D. B. Dahl, Richard D. Payne, Deepthi Uppalapati (2013), jvmr: Integration of R, Java, and Scala, , submitted. Paper.Journal of Statistical Software | |

xtable | An R package to export tabular data into LaTeX and HTML tables. | |

cortorgles | Software implementation of the methods described in: K. P. Lennox, D. B. Dahl, M. Vannucci, R. Day, J. W. Tsai (2010), A Dirichlet Process Mixture of Hidden Markov Models for Protein Structure Prediction, , 4, 916-962.
Paper.Annals of Applied Statistics | |

modalclust | Software implementation of the methods described in:
D. B. Dahl (2009), Modal Clustering in a Class of Product Partition Models, , 4, 243-264. Paper.Bayesian Analysis | |

RinRuby | Software described in:
D. B. Dahl, S. Crawford (2009), RinRuby: Accessing the R Interpreter from Pure Ruby, , 29(4), 1-18. Paper.Journal of Statistical Software | |

dbdexam | LaTeX package and helper program to generate many versions of a multiple choice exam with solutions and answer keys. | |

lsclust |
Software implementing the least squares clustering described in:
D. B. Dahl (2006), Model-Based Clustering for Expression Data via a Dirichlet Process Mixture Model, in , Kim-Anh Do, Peter Müller, Marina Vannucci (Eds.), Cambridge University Press.Bayesian Inference for Gene Expression and Proteomics |