# Publications in 2014-2015

**Publications, July 1, 2014 - June 30, 2015**

- Allen-Daniels, M.J., Serrano, M.G., Pflungner, L.P., Fettweis, J.M., Prestosa, M.A., Koparde, V.N.,
**Brooks, J.P.,**Strauss, III, J.F., Romero, R., Chaiworapongsa, T., Eschenbach, D.A., Buck, G.A., and Jefferson, K.K. (2015) "Identification of a Gene in Mycoplasma hominis Associated with Preterm Birth and Microbial Burden in Intra-amniotic Infection," American Journal of Obstetrics & Gynecology, 212, online ahead of print. **Boone, E. L., Merrick, J. R. W.**and Krachey, M. (2014) "A Hellinger distance approach to MCMC diagnostics," J. Stat. Comp. and Sim, Vol. 84, Nos. 4, 833-849.- Coleman, J. A., Ingram, K., Bays, A., Joy-Gaba, J. A., and
**Boone, E.L.**(2015) "Disability and Assistance Dog Implicit Association Test: A novel IAT," Rehabilitation Psychology. 60(1), 17–26. **Brooks, J.P., Edwards, D.J.,**Harwich, Jr., M.D., Rivera, M.C., Fettweis, J.M., Serrano, M.G., Reris, R.A., Sheth, N.U., Huang, B., Girerd, P., The Vaginal Microbiome Consortium (additional members), Strauss, J.F., III, Jefferson, K.K., and Buck, G.A. (2015) "The Truth about Metagenomics: Quantifying and Counteracting Bias in 16S rRNA Studies," BMC Microbiology, 15, 66.**Brooks, J.P**., Fettweis, J.M., Serrano, M.G., Girerd, P.H.,**Edwards, D.J.,**Strauss, J.F., Buck, G.A., Jefferson, K.K. (2014) "Differences in the vaginal microbiome and bacterial vaginosis in women of African versus European ancestry," Microbiology, 160, 2272-2282.**Brooks, J.P**., and Lee, E.K. (2014) "Solving a Mixed Integer Programming-Based Constrained Discrimination Model," INFORMS Journal on Computing, 26, 567-585.- Chen, Y.,
**Wang, Q.**and Yao, W. (2015) "Adaptive estimation for varying coefficient models," Journal of Multivariate Statistics, 137, 17-31. **Edwards, D.J.,**Weese, M.L. and Palmer, G.A. (2014) "Comparing Methods for Design Follow-up: Revisiting a Metal-Cutting Case Study," Applied Stochastic Models in Business and Industry, 30, 464-478.- Fettweis, J.M.,
**Brooks, J.P.,**Serrano, M.G., Sheth, N.U., Girerd, P.H.,**Edwards, D.J.,**Strauss, J.F., III, the Vaginal Microbiome Consortium, Jefferson, K.K., and Buck, G.A. (2014) "Differences in Vaginal Microbiome in African American Women versus Women of European Ancestry," Microbiology, 160, 2272-2282. - Fettweis, J.M., Serrano, M.G., Huang, B.,
**Brooks, J.P.,**Glascock, A.L., Sheth, N.U., Vaginal Microbiome Consortium, Strauss, J.F., Jefferson, K.K., and Buck, G.A. (2014) "An Emerging Mycoplasma Associated with Trichomoniasis, Vaginal Infection and Disease," PLOS ONE, 9(10), e110943. - Fukasawa, R., He, Q., and
**Song, Y**. (2014) "Energy Minimization Capacitated Vehicle Routing Problems," Accepted for publication, Transportation Science. - Huang, B., Fettweis, J.M.,
**Brooks, J.P.,**Jefferson, K.K., and Buck, G.A. (2014) "The Changing Landscape of the Vaginal Microbiome," Clinics in Laboratory Medicine, 34, 747-761. - The Integrative HMP Research Network Consortium (including Edwards, D.J. and Brooks, J.P.) (2014) "The Integrative Human Microbiome Project: Dynamic Analysis of Microbiome-Host Omics Profiles during Periods of Human Health and Disease," Cell Host and Microbe, 16(3), 276-289.
**Ly, C.**(2014) "Dynamics of Coupled Noisy Neural Oscillators with Heterogeneous Phase Resetting Curves," SIAM Journal on Applied Dynamical Systems, 13, 1733—1755.**Merrick, J. R. W**, Butler, J. C., Morrice, D. J. (2015) "Using Multiattribute Utility Theory to Avoid Bad Outcomes by Focusing on the Best Systems in Ranking and Selection," Accepted by Journal on Simulation, available online from February 27, 2015.**Merrick, J. R. W., Leclerc, P.**(2014) "Modeling Adversaries in Counter-terrorism Decisions Using Prospect Theory," Appeared in early view for Risk Analysis. Article first published online: 14 JUL 2014.**Song, Y**., Luedtke, J., and Kucukyavuz, S. (2014) "Chance-constrained Packing Problems," INFORMS Journal on Computing, 26(4), 735-747.**Song, Y.**and Luedtke, J. (2015) "An Adaptive Partition-based Approach for Solving Two-stage Stochastic Programs with Fixed Recourse," Accepted for publication, SIAM Journal on Optimization.**Song, Y.**and Zhang, M. (2015) "Chance-Constrained Multi-Terminal Network Design Problems," Accepted for publication, Naval Research and Logistics.- Vanee, N.,
**Brooks, J.P.,**Spicer, V., Krokhin, O., Wilkins, J.A., Deng, Y., and Fong, S.S. (2014) "Proteomics-based Metabolic Model and Metabolic Characterization of the Cellulolytic Bacterium Thermobifida fusca," BMC Systems Biology, 8, 86. **Wang, Q**. and Wu, R. (2015) "Semiparametric estimation for the time series of count data," Communications in Statistics: Theory and Methods, 44, 983-995.**Wang, Q**., Yin, X. and Critchley, F. (2015) "Dimension reduction based on Hellinger integral," Biometrika, 102, 95-106.- Weese, M.L., Smucker, B.J., and
**Edwards, D.J.**(2015) "Searching for Powerful Supersaturated Designs," Journal of Quality Technology, 47(1), 66-84. - Wilson, S. R., Leonard, R. D.,
**Edwards, D. J.,**Swieringa, K. A., and Murdoch, J. L. (2015) "Model Specification and Confidence Intervals for Voice Communication," Quality Engineering. In Press. - Young, T.M., León, R.V., Chen, C.H., Chen, W., Guess, F.M.,
**Edwards, D.J.**(2015) "Robustly Estimating Lower Percentiles when Observations are Costly," Quality Engineering. In Press.

**Reports and Proceedings, July 1, 2014 - June 30, 2015**

- Hess, E.J. and
**Brooks, J.P.**(2015) "The Support Vector Machine and Mixed Integer Linear Programming: Ramp Loss SVM with L1-Norm Regularization," Proceedings of the 14th INFORMS Computing Society Conference, Richmond, VA, 2015. - Reris, R.A., and
**Brooks, J.P**. (2015) "Principal Component Analysis and Optimization: A Tutorial," Proceedings of the 14th INFORMS Computing Society Conference, Richmond, VA, 2015. **Song, Y.**and Dinh, T. (2014) "Optimal Containment of Misinformation in Social Media: A Scenario-based Approach," Proceedings of CSoNet’14, Lecture Notes in Computer Science.- Stewart-Koster, B.,
**Boone, E.L.**and Sheldon F. (2014) "Statistical Investigation for Optimisa- tion of the Healthy Waterways Ecosystem Health Monitoring Program," Report to the Healthy Waterways Partnership, South-East Queensland.

**Books and Chapters, July 1, 2014 - June 30, 2015**

**Merrick, J. R. W.**, LeClerc, P., Trenkov, H., Olsen, R. (2015) "Outthinking the Terrorists,"*Breakthroughs in Risk Analysis*, Anthony Cox (Ed), Wiley.

# Publications in 2013-2014

**Publications, July 1, 2013 - June 30, 2014**

- Boyce, R. W., Willett, T. K., Jones, G. R. and
**Boone E. L**. (2014) "Race Comparisons in Police Officer Bench Press Strength over 12.5 Years," International Journal of Exercise Science, 7(2), Article 5. **Edwards, D. J.**and**Brooks, J. P.**(2014) "Alternative Foldover Plans for Two-Level Nonregular Designs," Communications in Statistics – Simulation and Computation, 43(1), 209-224.**Edwards, D. J.**, Guess, F. M., León, R. V., Young, T. M., and Crookston, K. A. (2014) "Improving Estimates of Critical Percentiles by Induced Censoring," Reliability Engineering and System Safety*,*123, 47-56.**Edwards, D. J.**and Kelly, K. M. (2014) "Selecting a D-optimal Follow-Up Design Among Candidate Choices," Quality Engineering*,*26, 233-245.**Edwards, D. J.**(2014) "Follow-up Experiments for Two-Level Fractional Factorial Designs Via Double Semifoldover," Metrika, 77,483-507*.***Ly, C.**(2013) "A Principled Dimension-Reduction Method for the Population Density Approach to Modeling Networks of Neurons with Synaptic Dynamics," Neural Computation, 25, 2682-2708.**Merrick, J. R. W.,**and Grabowski, M. (2013) "Decision Performance and Safety Performance: A Value Focused Thinking Study in the Oil Industry," Articles in Advance of Decision Analysis.- Pakyz, A., Jawahar, R.,
**Wang, Q.**and Spencer, H. (2014) "Medication risk factor associated with healthcare-associated clostridium diffcile infection: a multilevel model case control study among 64 US academic medical centers," - Seref, O.,
**Brooks, J. P.,**and Fong, S. S. (2013) "Decomposition of Flux Distributions into Metabolic Pathways," IEEE/ACM Transactions on Computational Biology and Bioinformatics, 10, 984-993. - Seref, O., Chaovalitwongse, W. A., and
**Brooks, J. P.**(2014) "Relaxing Support Vectors for Classification," Annals of Operations Research, 216, 229-255. - Shen, J., Gallagher, C., and
**Lu, Q**. (2014) "Detection of Multiple Undocumented Change-points Using Adaptive Lasso," Journal of Applied Statistics, 41, 1161–1173. - Sismour, E. N., Nellis, S. C., Newton, S. H.,
**Mays, D. P.**, and Fine, M. L. (2013) "An Experimental Study of the Consumption of Channel Catfish*Ictalurus punctatus*by Largemouth Bass*Micropterus salmoides*when Alternative Prey Are Available," Copeia, 2, 277-283. **Song, Y.**and Luedtke, J. (2013) "Branch-and-cut Approaches for Chance-constrained Formulations of Reliable Network Design Problems," Mathematical Programming Computation, 5(4), 397-432.- Srinivasan, S., Sorrell, T. P.,
**Brooks, J. P., Edwards, D. J**., and Diehl, R. L. (2013) "Workforce Assessment Method for an Urban Police Department: An Analytics Approach to Estimate Patrol Staffing," Policing: An International Journal of Police Strategies & Management, 36(4), 702-718. **Wang, Q.**and Wu, R. (2013) "Shrinkage estimation of partially linear single-index models," Statistics and Probability Letters*,*83, 2324-2331.- Zreikat, H. H., Harpe, S. E., Stattum, P. W.,
**Mays, D. P**., Essah, P. A., and Cheang, K. I. (2014) "Effect of Renin-Angiotensin System Inhibition on Cardiovascular Events in Older Hypertensive Patients with Metabolic Syndrome," Metabolism: Clinical and Experimental, 63(3): 392-399.

**Reports and Proceedings, July 1, 2013 - June 30, 2014**

**Merrick, J. R. W.**(2013) "Aggregation of Forecasts from Multiple Simulation Models," Proceedings the 2013 Winter Simulation Conference.- Nobles M. A., Sego L. H., Cooley S. K., Gosink L. J., Anderson R.M.,
**Hays S. E.**, and Tardiff M. F. (2013) "A Decision Theoretic Approach to Evaluate Radiation Detection Algorithms," Proceedings of the 2013 IEEE International Conference on Technologies for Homeland Security. 683-686. - Van Dorp, J. R., and
**Merrick, J. R. W.**(2013) "Vessel Traffic Risk Assessment (VTRA): Preventing Oil Spills from Large Ships and Barges In Northern Puget Sound & Strait of Juan de Fuca," Report to the Puget Sound Partnership. - Watkins, W. T., Song, W. Y.,
**Merrick, J. R. W**., Weiss, E., Hugo, G. D., Siebers, J. (2013), "Multi-criteria optimization for real-time planning of lung cancer radiotherapy," Proceedings of the American Association for Physicists in Medicine Annual Meeting.

**Books and Chapters, July 1, 2013 - June 30, 2014**

**Boone, E. L.,**Simmons, S. J. and Ricanek, K. (2013) "A Restricted Model Space Approach for the Detection of Quantitative Trait Loci using Markov Chain Monte Carlo Model Composition", Lecture notes in*Communications in Computer and Information Sciences*, Filipe J and Fred A Eds.. Volume 271, pp 101-114, Springer Berlin Heidelberg.**Hays**,**S.**, Shen, H. and Huang, J. (2013) "Applications of Functional Dynamic Factor Models", in*Topics in Applied Statistics: 2012 Symposium of the International Chinese Statistical Association*, eds. Mingxiu Hu, Yi Liu, and Jianchang Lin, Springer Science+Business Media: New York, 23-38.- Sabo, R. and
**Boone, E.L.**(2013)*Statistical Research Methods, A Guide for Non-Statisticians*, Springer, New York, ISBN 978–1–4614–8707–4. **Street IV, W. S., Mays, J. E.,**and Johnson, R. E. (2014)*A Guide to Statistical Thinking*, 6^{th}edition, W. H. Freeman and Company.

# Publications in 2012-2013

**Publications, July 1, 2012 - June 30, 2013**

- Altner, D.S. and
**Brooks, J.P.**(2012) "Coverings and matchings in*r*-partite hypergraphs," Networks, 59:349-410. **Boone, E.L**.,**Merrick, J.R.W.**and Krachey, M. (2012) "A Hellinger distance approach to MCMC diagnostics," Journal of Statistical Computational and Simulation.**Brooks, J.P.**(2012) "The Court of Appeals of Virginia uses Integer Programming and Cloud Computing to Schedule Sessions," Interfaces, 42:544-553.**Brooks, J.P.,**Burns, W.P., Fong, S.S., Gowen, C.M., and Roberts, S.B. (2012) "Gap detection for genome-scale constraint-based models," Advances in Bioinformatics, Article ID 876976, 10 pages.**Brooks, J.P.**and Dula, J.H. (2013) "The L1-norm best-fit hyperplane," Applied Mathematics Letters*,*26:51-55.**Brooks, J.P.,**Dula, J.H., and**Boone, E.L**. (2013) "A pure L1-norm principal component analysis," Computational Statistics and Data Analysis, 61:83-98.- Bullene, R.E.,
**Brooks, J.P., Boone, E.L.,**Lipchin, C., Sorrell, T.P., Stewart, C.R. (2013) "Uncertainty Quantification for a Middle East Water Supply System," Journal of Water Resources Planning and Management, 139:223-234. **Edwards, D.J.,**León, R.V., Young, T.M., Guess, F.M., and Crookston, K.A. (2012) "Comparison of Two Wood Plastic Composite Extruders Using Bootstrap Confidence Intervals on Measurements of Sample Failure Data," Quality Engineering*,*25(1):23-33.- Fettweis, J.M., Serrano, M.G., Sheth, N.U., Mayer, C.M., Glascock, A.L.,
**Brooks, J.P**., Jefferson, K.K. (2012) "Species-Level Classification of the Vaginal Microbiome, Vaginal Microbiome Consortium, and GA Buck," BMC Genomics*,*13:S17. **Hays, S.**, Shen, H. and Huang, J. (2012) "Functional Dynamic Factor Models with Application to Yield Curve Forecasting," Annals of Applied Statistics 6(3):870–894.- LaRosa, P.S.,
**Brooks, J.P.,**Deych, E.,**Boone, E.L**.,**Edwards, D. J**.,**Wang,****Q.**, Sodergen, E., Weinstock, G., and Shannon, W. D. (2012) "Hypothesis Testing and Power Calculations for Taxonomic-Based Human Microbiome Data," PLOS ONE, 7(12):e52078. **Lu, Q.**and Wang, X.L. (2012) "An Extended Cumulative Logit Model for Detecting a Shift in Frequencies of Sky-cloudiness Conditions," Journal of Geophysical Research Atmospheres, 117:1-11.- Sheldon, F, Petersen, E,
**Boone, E.L.,**Rolls, R., Leigh, C., Bunn, S. and Harch, B. (2012) "Identifying the spatial scale of land use that most strongly influences overall river ecosystem health score," Ecological Applications, 22:2188–2203. - Stewart-Koster, B.,
**Boone, E.L.,**Kennard, M.J., Sheldon, F., Bunn, S.E., Olden, J.D. (2013) "Incorporating ecological principles into statistical models for the prediction of species’ distribution and abundance," Ecography. 36:342-353. - The Human Microbiome Consortium (
**Brooks, J.P.**among authors) (2012) "Structure, function and diversity of the human microbiome in an adult reference population," Nature*,*486:207-214. - The Human Microbiome Consortium (
**Brooks, J.P.**among authors) (2012) "A framework for human microbiome research," Nature, 485:215-221. - Van Dorp, J.R. and
**Merrick, J.R.W.**(2012) "Vessel Traffic Risk Assessment (VTRA): Updating the 2005 VTRA GW/VCU MTS Simulation Model from VTOSS 2005 to VTOSS 2010 data". Report to the Makah Tribal Council. - Yao, W. and
**Wang, Q.**(2013) "Robust variable selection through MAVE," Computational Statistics and Data Analysis, 63:42-49.

**Reports and Proceedings, July 1, 2012 - June 30, 2013**

- Parnell, G., Burk, R. C.,
**Merrick, J. R. W**. (2013) "Intelligent Adversary Modeling of Homeland Security Networks". Proceedings of the 2013 Industrial and Systems Engineering Research Conference, A. Krishnamurthy and W.K.V. Chan, eds., San Juan, Puerto Rico, June 2013.

**Books and Chapters, July 1, 2012 - June 30, 2013**

**Hays, S.**, Shen, H., and Huang, J.Z., (2012) "Topics in Applied Statistics: 2012 Symposium of the International Chinese Statistical Association," Springer Proceedings in Mathematics and Statistics.- Miller, J. and
**Street, W.S. IV.**(2013) "Instructor’s Solution Manual and Test Bank for Moore and Notz’s STATISTICS: Concepts and Controversies", 8e, by W.H. Freeman and Company. ISBN: 1-4292-7760-2. **Street, W.S. IV**(2013) "Instructor’s Test Bank for use with Moore/Notz: STATISTICS: Concepts and Controversies*"*, 8e, by W.H. Freeman and Company. Software (CD-ROM & Blackboard). ISBN: 1-4292-7909-5.