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Gory, J., R. Herbei, and L. Kubatko, (2016). Bayesian inference of selection in the Wright-Fisher diffusion model, Statistical Applications in Genetics and Molecular Biology, 17. Link [Code]
Lu, Y., Herbei, R., Kurtek, S. (2017) Bayesian Registration of Functions with a Gaussian Process Prior. Journal of Computational and Graphical Statistics, 26, 894-904, DOI:10.1080/10618600.2017.1336444. Link
Herbei, R., Paul, R. and Berliner, L.M. (2017) Applying diffusion-based Markov chain Monte Carlo. https://doi.org/10.1371/journal.pone.0173453 [Code]
Hepler, S. A. and Herbei, R. (2017) A Monte Carlo approach to quantifying discrepancies between intractable posterior distributions. Journal of Statistical Computation and Simulation, 87, 1666-1683. http://dx.doi.org/10.1080/00949655.2017.1281277
Herbei, R., Rytel, A.L., Lyons, W.B., McKnight, D.M., Jaros, C., Gooseff, M. N. and Priscu, J.C. (2016) Hydrological Controls on Ecosystem Dynamics in Lake Fryxell, Antarctica. http://dx.doi.org/10.1371/journal.pone.0159038
Schneider, G., Craigmile, P. F. and Herbei, R. (2017) Maximum likelihood estimation for stochastic differential equations using sequential kriging-based optimization, Technometrics, 59, 178--188. http://dx.doi.org/10.1080/00401706.2016.1153522
Kubatko, L., Shah, P., Herbei, R., Gilchrist, M. (2016) A codon model of nucleotide substitution that includes the effects of selection related to codon usage and protein production rates, Molecular Phylogenetics and Evolution, 94, 290-297. https://doi.org/10.1016/j.ympev.2015.08.026
Spade, D., Herbei, R., Kubatko, L. (2015) Geometric ergodicity of a hybrid sampler for Bayesian inference of phylogenetic branch lengths. Mathematical Biosciences, 268, 9-21. https://doi.org/10.1016/j.mbs.2015.07.002
White, S. A. and Herbei, R. (2015) A Monte Carlo approach to quantifying model error in Bayesian parameter estimation. Computational Statistics and Data Analysis, 83, 168-181. Link https://doi.org/10.1016/j.csda.2014.10.008
Herbei, R. and Berliner, M. (2014) Estimating ocean circulation: an MCMC approach with approximated likelihoods via the Bernoulli factory. Journal of the American Statistical Association, 109, p. 944-954. Link
Chen, N., Giannakis, D., Herbei, R., Majda, A. (2014) An MCMC algorithm for parameter estimation for signals with hidden intermittent instability. SIAM Journal of Uncertainty Quantification, 2, 647-669. https://doi.org/10.1137/130944977
Spade, D., Herbei, R., Kubatko, L. (2014) A Note on the Relaxation Time of Two Markov Chains on Rooted Phylogenetic Tree Spaces. Statistics and Probability Letters, 84, p. 247-252. Link
Milliff, R., Fiechter, J., Leeds, W., Herbei, R., Wikle, C., Hooten, M., Moore, A., Powell, T., Brown, J. (2013) Uncertainty Management in Coupled Physical-Biological Lower-Trophic Level Ocean Ecosystem Models, Oceanography 26(4), p. 98-115, http://dx.doi.org/10.5670/oceanog.2013.78. Link
Wikle, C., Milliff, R., Herbei, R., Leeds, W. (2013) Modern Statistical Methods in Oceanography: A Hierarchical Perspective, Statistical Science, 28, p. 466-486. Link
Fiechter, J., Herbei, R., W. Leeds, Brown, J., Milliff, R., Wikle, C., Powel, T., Moore, A. (2013) A Bayesian parameter estimation method applied to a marine ecosystem model for the coastal Gulf of Alaska. Ecological Modelling. 258, p. 122-133. Link
Herbei, R. and Kubatko, L. (2013) Monte Carlo estimation of total variation distance of Markov chains on large spaces, with application to phylogenetics, Statistical Applications to Genetics and Molecular Biology, 12, p. 39-48. Link
Flegal, J. and Herbei, R. (2012) Exact sampling for intractable probability distributions via a Bernoulli factory. Electronic Journal of Statistics, 6, 10-37. Link
Herbei, R., Lyons, B., Laybourn-Parry, J., Gardner, C., Priscu, J., McKnight, D. (2010) Physiochemical Properties Influencing Biomass Abundance and Primary Production in Lake Hoare, Antarctica. Ecological Modelling, 221, p. 1184-1193. Link
Herbei, R., McKeague, I. W., (2009) Geometric ergodicity of hybrid samplers for ill-posed inverse problems. Scandinavian Journal of Statistics, 36, p. 839-853. Link
Herbei, R., (2009) A Bayesian Approach to Inverse Problems: An Introductions with Examples. The Annals of West University of Timisoara, 3, 67--82.
Herbei, R., McKeague, I. W., Speer, K. (2008) Gyres and Jets: inversion of tracer data for ocean circulation structure. J. Phys. Ocean., 38, p. 1180-1202. Link
Herbei, R., Wegkamp, M., (2006) Classification with reject option. Canadian Journal of Statistics, 34 pp. 709-721.
McKeague, I.W., Nicholls, G., Speer, K., Herbei, R. (2005). Statistical inversion of South Atlantic circulation in an abyssal neutral density layer. J. Mar. Research, 63, 683-704.
