John Hughes: Statistician
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John Hughes


Some of my past work focused on processive motor proteins and was featured in the August 23, 2013 ASPPH Friday Letter.

My current research interests include methods for high-dimensional dependent data, Bayesian methods, and statistical computing.

Submitted Articles

R. Frounfelker, G. String, V. Napier, S. Vankadari, and J. Hughes. The WASHpsych datasets: WASH insecurity and psychosocial wellbeing in Ivory Coast and Nigeria.

B. Kang, J. Hughes, and M. Haran. Fast Bayesian inference for mean-parameterized Conway–Maxwell–Poisson models.

J. Hughes. Toward improved inference for Krippendorff's Alpha agreement coefficient.

B. Kang, J. Hughes, and M. Haran. Measuring sample quality in algorithms for intractable normalizing function problems. arXiv preprint


A Concise Introduction to Object-Oriented Data Structures and Algorithm Analysis, 2006, Pearson.

Get the book for free here.

Book Chapters

M. Haran, J. Hughes, and B. S. Lee. Latent Gaussian models and computation for large spatial data. In S. Brooks, A. Gelman, G. Jones, and X. L. Meng, editors, Handbook of Markov Chain Monte Carlo, Handbooks of Modern Statistical Methods. Chapman & Hall/CRC, 2024. preprint

D. Musgrove, D. Young, J. Hughes, and L. E. Eberly. A sparse areal mixed model for multivariate outcomes, with an application to zero-inflated Census data. In N. Diawara, editor, Modern Statistical Methods for Spatial and Multivariate Data. Springer, 2019.

M. Bezener, L. E. Eberly, J. Hughes, G. Jones, and D. R. Musgrove. Bayesian spatiotemporal modeling for detecting neuronal activation via functional magnetic resonance imaging. In W. K. Hardle, H. H.–S. Lu, and X. Shen, editors, Handbook of Big Data Analytics, Springer Handbooks of Computational Statistics. Springer, 2018.

Peer-Reviewed Articles

J. Hughes. A Bayesian tour of binomial inference. Statistics and Probability Letters, 205:109974, 2024.

B. Kang, S. Goldlust, E. Lee, J. Hughes, S. Bansal, and M. Haran. Spatial distribution and determinants of childhood vaccination refusal in the United States. Vaccine, 41(20):3189–3195, 2023.

J. Hughes. A unified Gaussian copula methodology for spatial regression analysis. Nature Scientific Reports, 12:15915, 2022.

J. Hughes. Sklar's Omega: A Gaussian copula-based framework for assessing agreement. Statistics and Computing, 32(3):46, 2022.

J. Hughes. krippendorffsalpha: An R package for measuring agreement using Krippendorff’s Alpha coefficient. The R Journal, 13(1):413–425, 2021.

J. Hughes. On the occasional exactness of the distributional transform approximation for direct Gaussian copula models with discrete margins. Statistics and Probability Letters, 177:109159, 2021.

B. Blair, S. Brindley, J. Hughes, E. Dinkeloo, L. McKenzie, and J. Adgate. Measuring environmental noise from airports, oil and gas operations, and traffic with smartphone applications: Laboratory and field trials. Journal of Exposure Science and Environmental Epidemiology, 28:548–558, 2018.

B. Blair, J. Hughes, W. Allshouse, L. McKenzie, and J. Adgate. Truck and multi-vehicle truck accidents with injuries near Colorado oil and gas operations. International Journal of Environmental Research and Public Health, 15(9):1861, 2018.

M. Bezener, J. Hughes, and G. Jones. Bayesian spatiotemporal modeling using hierarchical spatial priors, with applications to functional magnetic resonance imaging (with discussion). Bayesian Analysis, 13(4):1261–1313, 2018.

L. McKenzie, B. Blair, J. Hughes, W. Allshouse, N. Blake, D. Helmig, P. Milmoe, H. Halliday, D. Blake, and J. Adgate. Ambient non-methane hydrocarbon levels along Colorado's Northern Front Range: Acute and chronic health risks. Environmental Science & Technology, 52(8):4514–4525, 2018.

P. Morgan, M. J. Nissi, J. Hughes, S. Mortazavi, and J. Ellermann. T2* mapping provides information that is statistically comparable to an arthroscopic evaluation of acetabular cartilage. Cartilage, 9(3):237–240, 2018.

E. Kurum, J. Hughes, R. Li, and S. Shiffman. Time-varying copula models for longitudinal data. Statistics and Its Interface, 11(2):203–221, 2018.

S. Elwir, A. Shaukat, M. Shaw, J. Hughes, and J. Colton. Variability in, and factors associated with, sizing of polyps by endoscopists at a large community practice. Endoscopy International Open, 5(08):E742–E745, 2017.

L. Henn, J. Hughes, E. Iisakka, J. Ellermann, S. Mortazavi, C. Ziegler, M. J. Nissi, and P. Morgan. Disease severity classification using quantitative magnetic resonance imaging data of cartilage in femoroacetabular impingement. Statistics in Medicine, 36:1491–1505, 2017.

D. J. Bond, A. C. Andreazza, J. Hughes, T. Dhanoa, I. J. Torres, J.–M. Kozicky, L. T. Young, A. Morgan, R. W. Lam, and L. N. Yatham. A longitudinal study of the relationships between mood symptoms, body mass index, and serum adipokines in bipolar disorder. Journal of Clinical Psychiatry, 78(4):441–448, 2017.

D. Bond, A. Andreazza, J. Hughes, T. Dhanoa, I. Torres, J. Kozicky, L. Young, R. Lam, and L. Yatham. Relationships between inflammation, elevated body mass index, and depressive relapse in bipolar disorder. European Neuropsychopharmacology, 27:S566–S567, 2017.

A. E. Bantle, L. S. Chow, L. M. Steffen, Q. Wang, J. Hughes, N. H. Durant, K. H. Ingram, J. P. Reis, and P. J. Schreiner. The association of Mediterranean diet and cardiorespiratory fitness with development of prediabetes and diabetes: The coronary artery risk development in young adults (CARDIA) study. BMJ Open Diabetes Research and Care, 4(1):e000229, 2016.

D. Musgrove, J. Hughes, and L. E. Eberly. Hierarchical copula regression models for areal data. Spatial Statistics, 17:38–49, 2016.

L. S. Chow, A. O. Odegaard, T. A. Bosch, A. E. Bantle, Q. Wang, J. Hughes, M. Carnethon, K. H. Ingram, N. Durant, C. E. Lewis, J. Ryder, C. M. Shay, A. S. Kelly, P. J. Schreiner. 20-year fitness trends in young adults and incidence of prediabetes/diabetes: the CARDIA study. Diabetologia, 1–7, 2016.

D. Bond, A. Andreazza, J. Hughes, J.–M. Kozicky, D. Taj, I. Torres, L. T. Young, R. Lam, and L. Yatham. Association of peripheral inflammation with body mass index and depressive relapse in bipolar disorder. Psychoneuroendocrinology, 65:76–83, 2016.

D. Musgrove, J. Hughes, and L. E. Eberly. Fast, fully Bayesian spatiotemporal inference for fMRI data. Biostatistics, 17(2):291–303, 2016.

E. Kurum, J. Hughes, and R. Li. A semivarying joint model for longitudinal binary and continuous outcomes. Canadian Journal of Statistics, 44(1):44–57, 2016.

P.–Y. Iroh Tam, J. S. Menk, J. Hughes, and S. L. Kulasingam. An ecological analysis of pertussis disease in Minnesota, 2009–2013. Epidemiology and Infection, 144(4):847–855, 2016.

D. Bond, A. Andreazza, J. Hughes, T. Dhanoa, I. Torres, J. Kozicky, L. Young, R. Lam, and L. Yatham. Relationships between mood symptoms, weight, and serum adipokines in early-stage bipolar disorder. Bipolar Disorders, 17, 2015.

D. Bond, A. Andreazza, J. Hughes, T. Dhanoa, I. Torres, J. Kozicky, L. Young, R. Lam, and L. Yatham. A measure of total peripheral inflammation is associated with weight and depressive relapse in early-stage bipolar disorder. Bipolar Disorders, 17, 2015.

E. J. Nelson, J. Hughes, J. M. Oakes, J. S. Pankow, and S. L. Kulasingam. Geospatial patterns of human papillomavirus vaccine uptake in Minnesota. BMJ Open, 5(8), 2015.

J. Hughes. copCAR: A flexible regression model for areal data. Journal of Computational and Graphical Statistics, 24(3):733–755, 2015.

N. Kohli, J. Hughes, C. Wang, C. Zopluoglu, Y. Chang, and M. Davison. Fitting a linear–linear piecewise growth mixture model with unknown knots: A comparison of two common approaches to inference. Psychological Methods, 20(2):259–275, 2015.

M. Nissi, S. Mortazavi, J. Hughes, P. Morgan, and J. Ellermann. T2* relaxation time of acetabular and femoral cartilage with and without intra-articular gadopentetate dimeglumine in patients with femoroacetabular impingement. American Journal of Roentgenology, 204(6):W695–W700, 2015.

E. J. Nelson, J. Hughes, J. M. Oakes, J. S. Pankow, and S. L. Kulasingam. Estimation of geographic variation in human papillomavirus vaccine uptake in men and women: An online survey using Facebook recruitment. Journal of Medical Internet Research, 16(9):e198, 2014.

J. Hughes. ngspatial: An R package for fitting the centered autologistic and sparse spatial generalized linear mixed models for areal data. The R Journal, 6(2):81–95, 2014.

N. B. Paulson, A. J. Gilbertsen, J. J. Dalluge, C. W. Welchlin, J. Hughes, W. Han, T. S. Blackwell, T. A. Laguna, and B. J. Williams. The arginine decarboxylase pathways of host and pathogen interact to impact inflammatory pathways in the lung. PLOS ONE, 9(10):e111441, 2014.

E. J. Nelson, J. Hughes, J. M. Oakes, B. Thyagarajan, J. S. Pankow, and S. L. Kulasingam. Human papillomavirus infection in women who submit self-collected vaginal swabs after internet recruitment. Journal of Community Health, 1–8, 2014.

E. J. Nelson, S. L. Kulasingam, and J. Hughes. Spatial patterns of human papillomavirus-associated cancers within the state of Minnesota, 1998–2007. Spatial and Spatiotemporal Epidemiology, 9:13–21, 2014.

C. Ziegler, J. Ellermann, M. Nissi, R. Goebel, J. Hughes, M. Benson, P. Holmberg, R. Frei, and P. Morgan. Acetabular cartilage assessment in patients with femoroacetabular impingement using T2* mapping with arthroscopic verification. Radiology, 271(2):512–523, 2014.

D. Shrivastava, L. Utecht, J. Tian, J. Hughes, and J. T. Vaughan. In vivo radiofrequency heating in swine in a 3T (123.2 MHz) birdcage whole-body coil. Magnetic Resonance in Medicine, 72(4):1141–1150, 2014.

J. Hughes, S. Shastry, W. O. Hancock, and J. Fricks. Estimating velocity for processive motor proteins with random detachment. Journal of Agricultural, Biological, and Environmental Statistics, 18(2):204–217, 2013.

J. Hughes and M. Haran. Dimension reduction and alleviation of confounding for spatial generalized linear mixed models. Journal of the Royal Statistical Society, Series B, 75(1):139–159, 2013.

D. Shrivastava, A. Abosch, J. Hughes, U. Goerke, L. DelaBarre, R. Visaria, N. Harel, and J. T. Vaughan. Heating induced near deep brain stimulation lead electrodes during magnetic resonance imaging with a 3T transceive volume head coil. Physics in Medicine and Biology, 57:5651–5665, 2012.

J. Hughes, W. O. Hancock, and J. Fricks. Kinesins with extended neck linkers: A chemomechanical model for variable-length stepping. Bulletin of Mathematical Biology, 74:1066–1097, 2012.

J. Hughes, M. Haran, and P. C. Caragea. Autologistic models for binary data on a lattice. Environmetrics, 22(7):857–871, 2011.

J. Hughes, W. O. Hancock, and J. Fricks. A matrix computational approach to kinesin neck linker extension. Journal of Theoretical Biology, 269(1):181–194, 2011.

J. Hughes and J. Fricks. A mixture model for quantum dot images of kinesin motor assays. Biometrics, 67(2):588–595, 2011.

J. Hughes, J. Fricks, and W. Hancock. Likelihood inference for particle location in fluorescence microscopy. The Annals of Applied Statistics, 4(2):830–848, 2010.