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Paul Joyce

Publications

• Approximately suffcient statistics and Bayesian computation.  P. Joyce, P. Marjoram.  Annals of Applied Statistics. (submitted). 
  

• Beneficial fitness effects are not exponential for two viruses. Rokyta  D. R ,C.J. Beisel, P. Joyce, and H. A.   Wichman. J. Mol. Evo.  (submitted) .

•  Simulation from a Normally Weighted Dirichlet Distribution. Genz, A. and P. Joyce.  Mathematics and Computers in Simulation  (submitted).
  

• An irrational constant separates selective under dominance from neutrality in the infinite alleles model. P. Joyce and F. Gao. (in preparation) .

• Evolution of diversity in spatially structured E. coli populations.  J.M. Ponciano, H.J, La .P. Joyce  and L.J. Forney.  Ecology (under revision)

• Efficient simulation methods for a class of nonneutral  population genetics models, P. Joyce and A. Genz. Theoretical Population Biology, (under revision) (pdf Preprint).

• Ordered vs. unordered samples: Response to Bromaghin, C.R. Miller,  P. Joyce  and L.P. Waits.  Molecular Ecology , 16: 4885, 2007.
  

•  Testing the extreme value domain of attraction for distributions of beneficial fitness effects.C.J. Beisel, D. R. Rokyta, H. A. Wichman, and P. Joyce. Genetics.176: 2441–2449,  2007.
  

•  High frequency of mutations that expand the host range of an RNA virus. M. T. Ferris, P.Joyce, and C. L Burch. Genetics. 176: 1013–1022,  2007.

• Differences in the composition of vaginal microbial communities found in healthy Caucasian and Black women
  X. Zhou, C. J. Brown, Z. Abdo, C.C. Davis, M. A. Hansmann, P. Joyce, J. A. Foster, and L. J. Forney.  International Society for Microbial Ecology Journal 1: 121-133, 2007.
  

•  The population biology of bacterial plasmids:  a Hidden-Markov model approach. J. M. Ponciano,  L. De Gleder, E. M. Top, P. Joyce. Genetics, 176: 957–968,  2007.

• Stability of a promiscuous plasmid in different hosts: No guarantees for a long-term association. L. De Gelder, J. M. Ponciano, P. Joyce and E. M. Top, Microbiology 153: 452-463, 2007.

•  Bayesian hierarchical error model for analysis of gene expression data.  X.L. Wu, L.J. Forney, and  P. Joyce Bioniformatics 22: 2446 - 2451, 2006.
  

• Phylogeography and mitochondrial diversity of extirpated brown bear (Ursus arctos) populations in the contiguous United States and Mexico .  C.R. Miller, L.P. Waits, and P. Joyce Molecular Ecology , 15, 4477–4485 , 2006. (pdf Reprint).

•  Properties of adaptive walks on uncorrelated landscapes under strong selection and weak mutation.  R. Rokyta, C.J. Beisel and P. Joyce.  Journal of Theoretical Biology , 243, (1), 114-120, 2006.

• Markov Chain Monte Carlo in small worlds.  G. Gaun, R. Fleissner, P. Joyce and S. Krone. Statistics and Computing  16, 193-202, 2006.   (pdf Preprint).
  

• Statistical methods for characterizing diversity in microbial communities by analysis of terminal restriction fragment length polymorphism of 16S rRNA.  Z. Abdo, U. Schuette, S.  Bent, C.  Williams,  L.J. Forney, and  P. Joyce.  Environmental Microbiology.  8 (5) , 929-938, 2006.

• Model selection in phylogenetics. J. Sullivan. and P. Joyce. Annual Reviews of Ecology, Evolution and Systematics, 36, 445-466, 2005.  (pdf Reprint)    (supplement)
  

• A new method for estimating the size of small populations from genetic mark-recapture data.  C.R. Miller, P. Joyce and L.P. Waits. Molecular Ecology 14, 1991-2005, 2005. (pdf Reprint)

• Testing population genetic structure using parametric bootstrapping and  MIGRATE-N . B.C Carstens, A.R. Bankhead III, P. Joyce, and J. Sullivan.  Genetica 124 , 71-75, 2005. (pdf Reprint)

• Evaluating the performance of a successive-approximations approach to parameter optimization in maximum-likelihood phylogeny estimation .  J. Sullivan, Z. Abdo, P. Joyce and D.L. Swofford. J. Mol. Bio. Evol. 22, (5), 1386-1392, 2005. (pdf Reprint).
  

• Use of stochastic models to assess the effect of environmental factors on microbial growth.   J. M. Ponciano, F. Vandecasteele, T. Hess, L. J. Forney, R.L. Crawford, and  P. Joyce. Applied Environmental Microbiology,  71 (5), 2355-2364, 2005. (pdf Reprint)
  

• An empirical test of the mutational landscape model of adaptive evolution using a ssDNA bacteriophage.  D.R. Rokyta, P.Joyce, S.B. Caudle, and H.A. Wichman.  Nature Genetics , 37  (4) 441-444, 2005. (pdf Reprint) (News and Views page 6)
  

• Accounting for uncertainty in the tree topology has little effect on the decision theoretic approach to model selection in phylogeny estimation.  Z. Abdo, V. Minin, P.  Joyce, J. Sullivan, J., Mol.  Bio. Evol. 22 (3), 691-703, 2005. (pdf Reprint)

• Modeling the impact of periodic bottlenecks unidirectional mutation and observational error in experimental evolution.  P. Joyce,  Z. Abdo, J. Ponciano, L. De Gelder, L. Forney,  and  E. Top.  J. Math. Bio..  50, (6) 645-662, 2005. (Online 2004)
  (pdf Reprint )

• Combining mathematical models and statistical methods to understand and predict the dynamics of antibiotic sensitive mutants in a population  of resistant bacteria during experimental evolution.   L. DeGelder, J. Ponciano, Z. Abdo, P. Joyce,  L. Forney and E. Top  Genetics. 168, (3), 1131-1144, 2004. (pdf Reprint)

• Evaluating the performance of likelihood methods for detecting population structure and migration. Z. Abdo, K.A. Crandall and P. Joyce Molecular Ecology , 13, 837-851, 2004. (pdf Reprint)

• Computation of the normalizing constant for exponentially weighted dirichlet distribution integrals. A.Genz and P. Joyce  Computing Science and Statistics, 35, 557-563, 2003. (pdf Preprint)
  

• Performance-based selection of likelihood models for phylogeny estimation.  V. Minin, Z. Abdo, P. Joyce, and J. Sullivan, . Systematic Biology, 52, (5), 672-684, 2003. (pdf Reprint)
  

• When can one detect overdominant selection in the infinite alleles model? P. Joyce, S. Krone  and T. Kurtz. Annals of Applied Probability, 13:181-212, 2003.   (pdf Reprint)

• Gaussian limits associated with the Poisson--Dirichlet distribution and the Ewens Sampling Formula. P. Joyce, Steve Krone and Tom Kurtz. Annals of Applied Probability, 12: 101-124, 2002.  (pdf Reprint)

• Assessing allelic dropout and genotype reliability using maximum likelihood. C. Miller, P. Joyce and L.Waits. Genetics, 160: 357-366, 2002. (pdf Reprint)
  

• Likelihood, simulation methods, and inference for a class of non-neutral population genetics models.  P. Donnelly, M. Nordborg, and P. Joyce , Genetics, 159: 853-867, 2001. (pdf Reprint) (Abstract).

• The power to detect recombination using the coalescent.   Celeste J. Brown, Ethan C. Garner, A. Keith Dunker., P. Joyce  J. Mol.  Bio. Evol, 18,(7): 1421-1424, 2001. (pdf Reprint)
  

• Linear estimators for the evolution of transposable elements, Proceedings of the American Mathematical Society (AMS), Institute of Mathematical Statistics (IMS), Society for Industrial and Applied Mathematics (SIAM) Joint Summer Research Conference in Statistics and Molecular Biology, F. Seillier Moiseiwitch and P. Donnelly eds. 33: 207-220, 1999 P. Joyce, C. Casavant, L. Fox, H. Wichman. (Abstract)

• No BLUE among phylogenetic estimators. P. Joyce J. Math. Bio.39 (5): 421-438,  1999. (Abstract)

• Partition structures and sufficient statistics.P. Joyce J. Appl. Prob. 35(3): 622-632, 1998. (Abstract)

• The distribution of rare alleles.P. Joyce and S. Tavaré J. Math. Bio. 33, 602-618,  1995.  (Abtract)

• Robustness of the Ewens Sampling Formula. P. Joyce, J.  Appl. Prob., 32, 609-622, 1995. (Abstract in pdf)

• Likelihood ratios and the infinite alleles model. P. Joyce, J. Appl. Prob., 31, 595-605, 1994. (Abstract in pdf)

• Weak convergence of population genealogical processes to a coalescent with ages.P. Donnelly and P. Joyce .Annals of Prob., 20, 322-341, 1992,. (Abstract)

• A convergence theorem for symmetric functionals of random partitions.P. Joyce and S. Tavaré Adv. Appl. Prob., 29, 280-290, 1992. . (Abstract in pdf).

• Consistent ordered sampling distributions, characterization and convergence. P. Donnelly and  P. Joyce Adv. Appl. Prob., 23, 229-258, 1991.
  

• Estimating the frequency of the oldest allele:  A Bayesian approach..P. Joyce  Adv. Appl. Prob. 23, 456-475, 1991.
  

• Random permutations and neutral evolution models. P. Joyce and S. Tavaré. Stoch. Proc. Applns.,36, 245-261, 1990.
  

• Is knowing the age-order of alleles useful in testing for selective neutrality?  W.J. Ewens, S. Tavaré and P. Joyce  Genetics, 122, 705-711, 1989.

• Continuity and weak convergence of ranked and size-biased permutations on an infinite simplex. P. Donnelly and P. Joyce Stoch. Proc. Applns., 31, 89-103, 1989.

• Cycles, permutations, and the structure of the Yule process with immigration. P. Joyce and S. Tavaré Stoch. Proc. Applns., 25, 309-314, 1987.