Susceptibility Testing and Prevalence Estimation

I collaborated with the Antimicrobial Susceptbility Testing Subcommittee of the National Committee of Clinical Laboratory Standards (NCCLS) 1998-2005 and then the Antimicrobial Susceptibility Subcommittee of the Clinical and Laboratory Standards Institute from 2008-2020. The focus was on ways to improve the current diameter breakpoint determination procedure (modified error-rate bounded method) and monitor resistance prevalence.  These papers summarizes this work. This research was supported in part by NIH (R01 AI48067-01A1).
 
• DePalma, G and Craig, BA (2018). Bayesian monotonic error-in-variables models with applications to pathogen susceptibility testing, Statistics in Medicine , 37(3), 487--502.
• DePalma, G, Turnidge, J, and Craig BA (2017). Determination of disk diffusion susceptibility testing interpretive criteria using model-based analysis: development and implementation, Diagnostic Microbiology and Infectious Disease, 87(2), 143--149.
• Xu, H, Black, M, and Craig, BA (2013). Evaluating Accuracy of Diagnostic Tests with Intermediate Results in the Absence of a Gold Standard, Statistics in Medicine, 32(15), 2571--2584.
• Annis, DH and Craig, BA (2005). The Effect of Inter-Laboratory Variability on Antimicrobial Susceptibility Determination. Diagnostic Medicine and Infectious Diseases , 53(1), 61-64.
• Annis, DH and Craig, BA (2005). Statistical properties and inference of the antimicrobial MIC test. Statistics in Medicine , 24(23), 3631-3644.
• Craig B.A. (2000). Modeling Approach to Breakpoint Determination, Diagnostic Microbiology and Infectious Disease, 36(3), 193-202.
• Black, M.A. and Craig, B.A. (2002). Estimating disease prevalence in the absence of a gold standard, Statistics in Medicine, 21(18), 2653-2669.
• Black, M.A., Jones, R.D., Carroll, G.J., Craig, B.A. (1999). A Bayesian approach to the assessment of diagnostic test accuracy in the absence of a gold standard. American Statistical Association, Proceedings of the Section on Statistics and Epidemiology, 94-98.

Protein Structure Determination

I have been collaborating with Dr. Alan Friedman (Biology, Purdue) and Dr. Chris Bailey-Kellogg (CS, Dartmouth) on a systematic framework for inference about structural properties of proteins on the basis of multimodal experimental data. This research is currently supported by NSF (5-34001.571).
 
• Vitek, O., Bailey-Kellogg, C., Craig, B.A., Vitek, J. (2006). Inferential Backbone Assignment for Sparse Data, Journal of Biomolecular NMR, online first, 1-22.
• Vitek, O., Bailey-Kellogg, Craig, B.A., Kuliniewicz, P. and Vitek, J. (2005). Reconsidering Complete Search Algorithms for Protein Backbone NMR Assignment, Bioinformatics, 21, ii230-ii236.
• Vitek, O., Vitek, J., Craig, B.A., and Bailey-Kellogg, C. (2004). Model-Based Assignment and Inference of Protein Backbone Nuclear Magnetic Resonances, Statistical Applications in Genetics and Molecular Biology , 3(1) , Article 6.

Bioinformatics

• Wang, C., Xie, J., and Craig, B.A. (2006). Context dependent models for discovery of transcription factor binding sites, Statistical Methodology , 3(1), 55-68.
• McFarlin, B.K., Flynn, M.G., Campbell, W.W., Craig, B.A., Robinson, J.P., Stewart, L.K., Timmerman, K.L., and Coen, P.M. (2006). Physical activity status, but not age, influences inflammatory biomarkers and toll-like receptor 4, Journal of Gerontology Series A-Biological Sciences & Medical Sciences , 61(4), 388-393.
• Mohammed, S.I., Dhawan, D., Abraham, S., Snyder, P.W., Waters, D.J., Craig, B.A., Lu, M., Wu, L., Zheng, R., Stewart, J., and Knapp, D.W. (2006). Cyclooxygenase inhibitors in urinary bladder cancer: in vitro and in vivo effects, Molecular Cancer Therapeutics , 5(2) , 329-336.
• Stewart, L.K., Flynn, M.G., Campbell, W.W., Craig, B.A., Robinson, J.P., McFarlin, B.K., Timmerman, K.L., Coen, P.M., Felker, J., and Talbert, E. (2005). Influence of exercise training and age on CD14+ cell-surface expression of toll-like receptor 2 and 4, Brain, Behavior, and Immunity, 19 , 389-397.

Disease Modeling

While at Wisconsin, I was fortunate to work with Dennis Fryback and Ronald and Barbara Klein on a disease modeling project. This led to my collaboration with Peter Sendi et al. Much of this research is funded in some part by a NEI small research grant concerning the modeling of diabetic retinopathy.
 
• Liu, Y. and Craig, B.A. (2005). Incorporating time-dependent covariates in survival analysis using the LVAR method. Statistics in Medicine, 25(10), 1729-1740.
• Craig B.A. and Sendi P. (2002). Estimation and Uncertainty of the transition matrix of a homogeneous Markov chain, Health Economics, 11(1), 33-42.
• Sendi, P., Palmer, A.J., Hauri, P., Craig, B.A., Horber, F.F. (2002). Modeling the impact of adjustable gastric banding on survival in patients with morbid obesity, Obesity Research, 10, 291-295.
• Mohammed, S.I., Bennett, P.F., Glickman, N.W., Mutsaers, A.J., Snyder, P.W., Craig, B.A., Widmer, W.R., DeGortari, A.E., Bonney, P.I., and Knapp, D.W. (2002). Effect of the cyclooxygenase inhibitor, piroxicam, on tumor response, apoptosis, and angiogensis in canine model of human invasive urinary bladder cancer, Cancer Research , 62(2), 356-358.
• Craig B.A. and Black, M.A. (2001). Incremental cost-effectivness ratio and incremental net-health benefit: two sides of the same coin. Expert Review of Pharmacoeconomics & Outcomes Research, 1(1), 37-46.
• Craig, B.A., Black, M.A., and Sendi, P.P. (2000). Uncertainty in decision models analyzing cost effectiveness: A comment, Medical Decision Making , 20(1), 135-136.
• Craig B.A., Fryback D.G., Klein R, and Klein B.E.K. (1999). A Bayesian approach to modeling the natural history of a chronic condition from observations with intervention. Statistics in Medicine, 18, 1355-1371.
• Sendi, P.P., Craig, B.A., Meier, G., Pfluger, D., Gafni, A., Opravil, M., Battegay, M., Bucher, H.C. (1999). Cost effectiveness of azithromycin for preventing Mycobacterium avium complex infection in HIV-positive patients in the era of highly active antiretroviral, J Antimicrobial Chemotherapy , 44, 811-817.
• Sendi P.P., Bucher H.C., Harr T., Craig B.A., Schwietert M., Pfluger D., Gafni A., and Battegay M. (1999). Cost effectiveness of highly active antiretroviral therapy in HIV infected patients, AIDS , 13, 1115-1122.
• Sendi P.P., Craig B.A., Pfluger D., Gafni A., Bucher H.C. (1999). Systematic validation of disease models for pharmacoeconomic evaluations. Journal of Evaluation in Clinical Practice , 5 , 283-295.
• Sendi P.P., Bucher H.C., Craig B.A., Pfluger D., and Battegay M. (1999). Estimating AIDS-free survival in a severely immunosuppressed asymptomatic HIV-infected population in the era of antiretroviral triple combination therapy, Journal of Acquired Immunedeficiency Syndromes and Human Retrivirology, 20 , 376-381.
• Craig, B.A. and Newton, M.A. (1997). Modeling the history of diabetic retinopathy in Case Studies in Bayesian Statistics III, C. Gatsonis et al. eds, New York: Springer-Verlag, 305--323.
• Mehta, M.P., Noyes, W.R., Craig, B.A., Lamond, J.P., Auchter, R.M., French, M.C., Johnson, M.N., Levin, A.B., Badie, B., Robins, H.I., and Kinsella, T.K. (1997). A cost-effectiveness and cost-utility analysis of radiosurgery versus resection for single brain metastases, International Journal of Radiation Oncology, Biology, Physics, 39 , 445--454.
• Noyes W.R., Mulcahy, R.T., Craig B.A., and Kinsella T.J. (1996). The effect of a pure anti-estrogen, ICI 182,780, on the in vitro radiosensitivity of MCF-7 breast carcinoma cells, Radiation Oncology Investigations, 3, 232-237.

Design and Analysis of Gene Expression Data

• Craig, B.A. (2005). Discussion of Semilinear high-dimensional model for normalization of microarray data: a theoretical analysis and partial consistency, Journal of the American Statistical Society, 100, 799-800.
• B.A. Craig, M.A. Black, and R.W. Doerge. (2003). Gene Expression Data: The technology and statistical analysis, Journal of Agricultural, Biological, and Environmental Statistics (JABES), 8(1) :1-28.
• Fleet, J.C., Wang, L., Vitek, O., Craig, B.A., and Edenberg, H.J. (2003). Gene expression profiling of Caco-2 BBe cells suggests a role for specific signaling pathways during intestinal differentiation Physiol. Genomics , 10.1152/physiolgenomics.00152.2002.
• Craig, B.A., Vitek, O., Black, M.A., Tanurdzic, M., and Doerge, R.W. (2002). Designing Microarrays, in Proceedings of the 2001 Kansas State University Conference on Applied Statistics in Agriculture, G.A. Milliken ed., Manhattan, KS: Department of Statistics, 159-182.

QTL Analysis in Polyploids

• Cao, D., Craig, B.A., and Doerge, R.W. (2005). A maximum likelihood based interval mapping method for autopolyploids. Genetics , 169(4), 2371-2382.
• Cao, D., Craig, B.A., and Doerge, R.W. (2005). Bayesian Quantitative Trait Mapping for Autopolyploids. Proceedings of the 2004 Kansas State University Conference on Applied Statistics in Agriculture, G.A. Milliken ed., Manhattan, KS : Department of Statistics, 172-186.
• Cao, D., Craig, B.A., and Doerge, R.W. (2004). Interval Mapping for Autopolyploids. Proceedings of the 2003 Kansas State University Conference on Applied Statistics in Agriculture, G.A. Milliken ed., Manhattan, KS : Department of Statistics, 60-69.
• Doerge, R.W. and Craig, B.A. (2001). An introduction to model selection for quantitative trait locus analysis in polyploids. Proceedings of the 2000 Kansas State University Conference on Applied Statistics in Agriculture , 13-27.
• Doerge, R.W. and Craig, B.A. (2000). Model selection for quantitative trait locus analysis in polyploids. Proceedings of the National Academy of Science, 97(14) , 7951-7956.

Population Dynamics

• Craig, B.A. and Reynolds III, J.E. (2004). Determination of manatee population trends using a Bayesian approach with temperature-adjusted aerial survey data, Marine Mammal Science, 20 , 386-400.
• Gross, K., Craig, B.A., and Hutchison, W.D. (2002). Bayesian estimation of a demographic matrix model from stage-frequency data, Ecology , 83(12), 3285-3298.
• Craig, B.A., Newton, M.A., Garrott, R.A., Reynolds III, J.E. and Wilcox, J.R. (1997). Analysis of aerial survey data on Florida Manatee using Markov chain Monte Carlo. Biometrics, 53(2), 129-146.

Biodiversity

• Craig, B.A., Gu, W. and Feng, Z. (2003). Developing an integrated model of land-use/land-cover change, in R.K. Swihart and J.E. Moore, eds. Conserving biodiversity in agricultural landscapes: model-based planning tools. Purdue University Press, West Lafayette, Indiana. In press.
• DeWoody, Y., Swihart, R.K., Craig, B.A., and Goheen, J.R. (2003). Diversity and Stability in Communities Structured by Asymmetric Resource Allocation, American Naturalist , 162(4), 514-527.

Crack Growth Modeling

• Laz, P.J., Hillberry, B.M., and Craig, B.A. (2001). A probabilistic total fatigue life model incorporating stress level, International Journal of Fatigue, 23 S119-S127.
• van der Walde, K. Brockenbrough, J.R., Craig B.A., Hillberry, B.M. (2005). Multiple fatigue crack growth in pre-corroded 2024-T3 aluminum, International Journal of Fatigue , 27 , 1509-1518.
• Laz, P.J., Craig, B.A., Rohrbaugh, S. M. and Hillberry, B.M. (1999). The development of a total fatigue life approach accounting for nucleation and propagation. Fatigue '99 : Proceedings of the Seventh International Fatigue Congress, 2, 833-838.
• Gruenberg K.M., Craig B.A., Hillberry B.M., Bucci R.J., and Hinkle A.J. (2004). Predicting fatigue life of pre-corroded 2024-T3 aluminum from breaking load tests. International Journal of Fatigue, 26 , 615-627.
• Gruenberg K.M., Craig B.A., Hillberry B.M., Bucci R.J., and Hinkle A.J. (2004). Predicting fatigue life of pre-corroded 2024-T3 aluminum. International Journal of Fatigue , 26, 629-640.
• Hillberry, B.M., Laz, P.J., Gruenberg, K.M., Debartolo E.A., and Craig, B.A. (1999). Inherent material behavior and widespread fatigue. Fatigue '99 : Proceedings of the Seventh International Fatigue Congress, 4, 2539-2544.
• Gruenberg K.M., Craig B.A., and Hillberry B.M. (1999). A probabilistic method for predicting the variability in fatigue behavior of 7075-T6 aluminum, Journal of the American Institute of Aeronautics and Astronautics, 37, 1304-1310.

Nonlinear Mixed Models

• Schinckel, A.P. and Craig, B.A. (2002). Evaluation of Alternative Nonlinear Mixed Effects Models of Swine Growth, The Professional Animal Scientist , 18, 219-226.
• Craig, B.A. and Schinckel, A.P. (2001). Nonlinear mixed effects model for swine growth, The Professional Animal Scientist , 17(4), 256-260.
• Weigel K.A., Craig B.A., Bidwell T.R., Bates, D.M., (1992). Comparisons of alternative diphasic curve models under bovine somatotropin administration, Journal of Dairy Science, 75, 580-589.

Other

• Annis, D.H. and Craig, B.A. (2005). Hybrid Paired Comparison Analysis, with Applications to the Ranking of College Football Teams, Journal of Quantitative Analysis in Sports , 1(1), Article 3.
• Eberts, C., Eberts R., and Craig, B. (1999). Interactive Remedial Statistics Learning Modules for the Internet. Proceeedings of the Human Factors and Ergonomics Society, 43 , 530-534.
• Burr, A.F., Craig, B.A., Chung, C-G, So, T-S. H., Deveau, T.J., and Shirer, D.L. (1999). Programs for Statistics and Data Analysis, Computing in Science and Engineering, 1(1), 17-21.

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