Paul Joyce - Publications

Affiliations: 
University of Idaho, Moscow, ID, United States 
Area:
Biostatistics Biology

49 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2017 Miller CR, Van Leuven JT, Wichman HA, Joyce P. Selecting among three basic fitness landscape models: Additive, multiplicative and stickbreaking. Theoretical Population Biology. PMID 29198859 DOI: 10.1016/j.tpb.2017.10.006  0.36
2017 Joyce P, Abdo Z. Determining the distribution of fitness effects using a generalized Beta-Burr distribution. Theoretical Population Biology. PMID 28709927 DOI: 10.1016/j.tpb.2017.07.001  1
2016 Nardin LG, Miller CR, Ridenhour BJ, Krone SM, Joyce P, Baumgaertner BO. Planning horizon affects prophylactic decision-making and epidemic dynamics. Peerj. 4: e2678. PMID 27843714 DOI: 10.7717/peerj.2678  0.36
2016 Miller CR, Nagel AC, Scott L, Settles M, Joyce P, Wichman HA. Love the one you're with: replicate viral adaptations converge on the same phenotypic change. Peerj. 4: e2227. PMID 27547540 DOI: 10.7717/peerj.2227  1
2016 Baker CW, Miller CR, Thaweethai T, Yuan J, Hollibaugh Baker M, Joyce P, Weinreich DM. Genetically Determined Variation in Lysis Time Variance in the Bacteriophage ϕX174. G3 (Bethesda, Md.). PMID 26921293 DOI: 10.1534/g3.115.024075  1
2015 Wojtowicz AJ, Miller CR, Joyce P. Inference for one-step beneficial mutations using next generation sequencing. Statistical Applications in Genetics and Molecular Biology. 14: 65-81. PMID 25720101 DOI: 10.1515/sagmb-2014-0030  1
2013 Bull JJ, Joyce P, Gladstone E, Molineux IJ. Empirical complexities in the genetic foundations of lethal mutagenesis. Genetics. 195: 541-52. PMID 23934886 DOI: 10.1534/genetics.113.154195  1
2013 Tyerman JG, Ponciano JM, Joyce P, Forney LJ, Harmon LJ. The evolution of antibiotic susceptibility and resistance during the formation of Escherichia coli biofilms in the absence of antibiotics. Bmc Evolutionary Biology. 13: 22. PMID 23356665 DOI: 10.1186/1471-2148-13-22  1
2013 Bataillon T, Joyce P, Sniegowski P. As it happens: current directions in experimental evolution. Biology Letters. 9: 20120945. PMID 23118431 DOI: 10.1098/rsbl.2012.0945  1
2012 Wojtowicz AJ, Miller CR, Joyce P. Estimating the number of one-step beneficial mutations. Statistical Applications in Genetics and Molecular Biology. 11. PMID 22850060 DOI: 10.1515/1544-6115.1788  1
2012 Joyce P, Genz A, Buzbas EO. Efficient simulation and likelihood methods for non-neutral multi-allele models. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 19: 650-61. PMID 22697240 DOI: 10.1089/cmb.2012.0033  1
2012 Slater GJ, Harmon LJ, Wegmann D, Joyce P, Revell LJ, Alfaro ME. Fitting models of continuous trait evolution to incompletely sampled comparative data using approximate Bayesian computation. Evolution; International Journal of Organic Evolution. 66: 752-62. PMID 22380438 DOI: 10.1111/j.1558-5646.2011.01474.x  1
2012 Nagel AC, Joyce P, Wichman HA, Miller CR. Stickbreaking: a novel fitness landscape model that harbors epistasis and is consistent with commonly observed patterns of adaptive evolution. Genetics. 190: 655-67. PMID 22095084 DOI: 10.1534/genetics.111.132134  1
2011 Eastman JM, Alfaro ME, Joyce P, Hipp AL, Harmon LJ. A novel comparative method for identifying shifts in the rate of character evolution on trees. Evolution; International Journal of Organic Evolution. 65: 3578-89. PMID 22133227 DOI: 10.1111/j.1558-5646.2011.01401.x  1
2011 Lee KH, Miller CR, Nagel AC, Wichman HA, Joyce P, Ytreberg FM. First-step mutations for adaptation at elevated temperature increase capsid stability in a virus. Plos One. 6: e25640. PMID 21980515 DOI: 10.1371/journal.pone.0025640  1
2011 Rokyta DR, Joyce P, Caudle SB, Miller C, Beisel CJ, Wichman HA. Epistasis between beneficial mutations and the phenotype-to-fitness Map for a ssDNA virus. Plos Genetics. 7: e1002075. PMID 21655079 DOI: 10.1371/journal.pgen.1002075  1
2011 Buzbas EO, Joyce P, Rosenberg NA. Inference on the strength of balancing selection for epistatically interacting loci. Theoretical Population Biology. 79: 102-13. PMID 21277883 DOI: 10.1016/j.tpb.2011.01.002  1
2011 Miller CR, Joyce P, Wichman HA. Mutational effects and population dynamics during viral adaptation challenge current models. Genetics. 187: 185-202. PMID 21041559 DOI: 10.1534/genetics.110.121400  1
2009 Ponciano JM, La HJ, Joyce P, Forney LJ. Evolution of diversity in spatially structured Escherichia coli populations. Applied and Environmental Microbiology. 75: 6047-54. PMID 19648364 DOI: 10.1128/AEM.00063-09  1
2009 Buzbas EO, Joyce P, Abdo Z. Estimation of selection intensity under overdominance by Bayesian methods. Statistical Applications in Genetics and Molecular Biology. 8: Article32. PMID 19572831 DOI: 10.2202/1544-6115.1466  1
2009 Buzbas EO, Joyce P. Maximum likelihood estimates under k-allele models with selection can be numerically unstable Annals of Applied Statistics. 3: 1147-1162. DOI: 10.1214/09-AOAS237  1
2008 Huelsenbeck JP, Joyce P, Lakner C, Ronquist F. Bayesian analysis of amino acid substitution models. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 363: 3941-53. PMID 18852098 DOI: 10.1098/rstb.2008.0175  1
2008 Joyce P, Rokyta DR, Beisel CJ, Orr HA. A general extreme value theory model for the adaptation of DNA sequences under strong selection and weak mutation. Genetics. 180: 1627-43. PMID 18791255 DOI: 10.1534/genetics.108.088716  1
2008 Rokyta DR, Beisel CJ, Joyce P, Ferris MT, Burch CL, Wichman HA. Beneficial fitness effects are not exponential for two viruses. Journal of Molecular Evolution. 67: 368-76. PMID 18779988 DOI: 10.1007/s00239-008-9153-x  1
2007 Zhou X, Brown CJ, Abdo Z, Davis CC, Hansmann MA, Joyce P, Foster JA, Forney LJ. Differences in the composition of vaginal microbial communities found in healthy Caucasian and black women. The Isme Journal. 1: 121-33. PMID 18043622 DOI: 10.1038/ismej.2007.12  1
2007 Beisel CJ, Rokyta DR, Wichman HA, Joyce P. Testing the extreme value domain of attraction for distributions of beneficial fitness effects. Genetics. 176: 2441-9. PMID 17565958 DOI: 10.1534/genetics.106.068585  1
2007 Ferris MT, Joyce P, Burch CL. High frequency of mutations that expand the host range of an RNA virus. Genetics. 176: 1013-22. PMID 17409090 DOI: 10.1534/genetics.106.064634  1
2007 De Gelder L, Ponciano JM, Joyce P, Top EM. Stability of a promiscuous plasmid in different hosts: no guarantee for a long-term relationship. Microbiology (Reading, England). 153: 452-63. PMID 17259616 DOI: 10.1099/mic.0.2006/001784-0  1
2007 Ponciano JM, De Gelder L, Top EM, Joyce P. The population biology of bacterial plasmids: a hidden Markov model approach. Genetics. 176: 957-68. PMID 17151258 DOI: 10.1534/genetics.106.061937  1
2006 Miller CR, Waits LP, Joyce P. Phylogeography and mitochondrial diversity of extirpated brown bear (Ursus arctos) populations in the contiguous United States and Mexico. Molecular Ecology. 15: 4477-85. PMID 17107477 DOI: 10.1111/j.1365-294X.2006.03097.x  1
2006 Rokyta DR, Beisel CJ, Joyce P. Properties of adaptive walks on uncorrelated landscapes under strong selection and weak mutation. Journal of Theoretical Biology. 243: 114-20. PMID 16859714 DOI: 10.1016/j.jtbi.2006.06.008  1
2006 Wu XL, Forney LJ, Joyce P. Comments on 'Bayesian hierarchical error model for analysis of gene expression data'. Bioinformatics (Oxford, England). 22: 2446-51; author repl. PMID 16731698 DOI: 10.1093/bioinformatics/btl173  1
2006 Abdo Z, Schüette UM, Bent SJ, Williams CJ, Forney LJ, Joyce P. Statistical methods for characterizing diversity of microbial communities by analysis of terminal restriction fragment length polymorphisms of 16S rRNA genes. Environmental Microbiology. 8: 929-38. PMID 16623749 DOI: 10.1111/j.1462-2920.2005.00959.x  1
2006 Guan Y, Fleißner R, Joyce P, Krone SM. Markov chain Monte Carlo in small worlds Statistics and Computing. 16: 193-202. DOI: 10.1007/s11222-006-6966-6  1
2005 Carstens BC, Bankhead A, Joyce P, Sullivan J. Testing population genetic structure using parametric bootstrapping and MIGRATE-N. Genetica. 124: 71-5. PMID 16011004  0.48
2005 Miller CR, Joyce P, Waits LP. A new method for estimating the size of small populations from genetic mark-recapture data. Molecular Ecology. 14: 1991-2005. PMID 15910321 DOI: 10.1111/j.1365-294X.2005.02577.x  1
2005 Ponciano JM, Vandecasteele FP, Hess TF, Forney LJ, Crawford RL, Joyce P. Use of stochastic models to assess the effect of environmental factors on microbial growth. Applied and Environmental Microbiology. 71: 2355-64. PMID 15870322 DOI: 10.1128/AEM.71.5.2355-2364.2005  1
2005 Rokyta DR, Joyce P, Caudle SB, Wichman HA. An empirical test of the mutational landscape model of adaptation using a single-stranded DNA virus. Nature Genetics. 37: 441-4. PMID 15778707 DOI: 10.1038/ng1535  1
2005 Sullivan J, Abdo Z, Joyce P, Swofford DL. Evaluating the performance of a successive-approximations approach to parameter optimization in maximum-likelihood phylogeny estimation. Molecular Biology and Evolution. 22: 1386-92. PMID 15758203 DOI: 10.1093/molbev/msi129  1
2005 Joyce P, Abdo Z, Ponciano JM, De Gelder L, Forney LJ, Top EM. Modeling the impact of periodic bottlenecks, unidirectional mutation, and observational error in experimental evolution. Journal of Mathematical Biology. 50: 645-62. PMID 15614551 DOI: 10.1007/s00285-004-0300-8  1
2005 Abdo Z, Minin VN, Joyce P, Sullivan J. Accounting for uncertainty in the tree topology has little effect on the decision-theoretic approach to model selection in phylogeny estimation. Molecular Biology and Evolution. 22: 691-703. PMID 15548751 DOI: 10.1093/molbev/msi050  1
2004 De Gelder L, Ponciano JM, Abdo Z, Joyce P, Forney LJ, Top EM. 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. Genetics. 168: 1131-44. PMID 15579675 DOI: 10.1534/genetics.104.033431  1
2004 Abdo Z, Crandall KA, Joyce P. Evaluating the performance of likelihood methods for detecting population structure and migration. Molecular Ecology. 13: 837-51. PMID 15012759 DOI: 10.1111/j.1365-294X.2004.02132.x  1
2003 Minin V, Abdo Z, Joyce P, Sullivan J. Performance-based selection of likelihood models for phylogeny estimation. Systematic Biology. 52: 674-83. PMID 14530134 DOI: 10.1080/10635150390235494  1
2003 Joyce P, Krone SM, Kurtz TG. When can one detect overdominant selection in the infinite-alleles model? Annals of Applied Probability. 13: 181-212.  1
2002 Miller CR, Joyce P, Waits LP. Assessing allelic dropout and genotype reliability using maximum likelihood. Genetics. 160: 357-66. PMID 11805071  1
2002 Joyce P, Krone SM, Kurtz TG. Gaussian limits associated with the poisson-dirichlet distribution and the Ewens sampling formula Annals of Applied Probability. 12: 101-124. DOI: 10.1214/aoap/1015961157  1
2001 Araji AA, Abdo ZO, Joyce P. Efficient use of animal manure on cropland--economic analysis. Bioresource Technology. 79: 179-91. PMID 11480927 DOI: 10.1016/S0960-8524(01)00042-6  1
2001 Brown CJ, Garner EC, Dunker AK, Joyce P. The power to detect recombination using the coalescent. Molecular Biology and Evolution. 18: 1421-4. PMID 11420381  1
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