selected publications
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academic article
- Selecting among three basic fitness landscape models: Additive, multiplicative and stickbreaking. Theoretical Population Biology. 122:97-109. 2018
- Determining the distribution of fitness effects using a generalized Beta-Burr distribution. Theoretical Population Biology. 122:88-96. 2018
- Love the one you're with: replicate viral adaptations converge on the same phenotypic change. PeerJ. 4. 2016
- Planning horizon affects prophylactic decision-making and epidemic dynamics. PeerJ. 4. 2016
- Genetically Determined Variation in Lysis Time Variance in the Bacteriophage φX174. G3: Genes Genomes Genetics. 6:939-955. 2016
- Inference for one-step beneficial mutations using next generation sequencing. Statistical Applications In Genetics and Molecular Biology. 14:65-81. 2015
- As it happens: current directions in experimental evolution. Biology Letters. 9. 2013
- Complexities in the Genetic Foundations of Lethal Mutagenesis. Genetics. 2013
- Empirical complexities in the genetic foundations of lethal mutagenesis. Genetics. 9. 2013
- The evolution of antibiotic susceptibility and resistance during the formation of Escherichia coli biofilms in the absence of antibiotics. Bmc Evolutionary Biology. 13. 2013
- Efficient Simulation and Likelihood Methods for Non-Neutral Multi-Allele Models. Journal of Computational Biology. 19:650-661. 2012
- Estimating the Number of One-step Beneficial Mutations. Statistical Applications In Genetics and Molecular Biology. 11. 2012
- Fitting Models of Continuous Trait Evolution to incompletely Sampled Comparative Data Using Approximate Bayesian Computation. Evolution. 66:752-762. 2012
- Stickbreaking: A Novel Fitness Landscape Model That Harbors Epistasis and Is Consistent With Commonly Observed Patterns of Adaptive Evolution. Genetics. 190:655-667. 2012
- A Novel Comparative Method for Identifying Shifts in the Rate of Character Evolution on Trees. Evolution. 65:3578-3589. 2011
- First-Step Mutations for Adaptation at Elevated Temperature Increase Capsid Stability in a Virus. PLOS ONE. 6. 2011
- Epistasis Between Beneficial Mutations and The Phenotype-to-fitness Map For A Ssdna Virus. PLOS Genetics. 7. 2011
- Inference on the strength of balancing selection for epistatically interacting loci. Theoretical Population Biology. 79:102-113. 2011
- Mutational Effects and Population Dynamics During Viral Adaptation Challenge Current Models. Genetics. 187:185-202. 2011
- The Onion Model, a Simple Neutral Model for the Evolution of Diversity in Bacterial Biofilms. Journal of Evolutionary Biology. 24:2496-2504. 2011
- Estimation of Selection Intensity under Overdominance by Bayesian Methods. Statistical Applications In Genetics and Molecular Biology. 8. 2009
- Evolution of Diversity in Spatially Structured Escherichia coli Populations. Applied and Environmental Microbiology. 75:6047-6054. 2009
- Maximum likelihood estimates under k-allele models with selection can be numerically unstable. Annals of Applied Statistics. 3:1147-1162. 2009
- Bayesian analysis of amino acid substitution models. Philosophical Transactions of the Royal Society B: Biological Sciences. 363:3941-3953. 2008
- Beneficial Fitness Effects Are Not Exponential For Two Viruses. Journal of Molecular Evolution. 67:368-376. 2008
- Approximately sufficient statistics and Bayesian computation. Statistical Applications In Genetics and Molecular Biology. 7. 2008
- A General Extreme Value Theory Model for the Adaptation of DNA Sequences Under Strong Selection and Weak Mutation. Genetics. 180:1627-1643. 2008
- A convergence theorm for symmetrical functions of random partitions. Journal of Applied Probability. 29:280-290. 2008
- Differences in the composition of vaginal microbial communities found in healthy Caucasian and black women.. The ISME (International Society for Microbial Ecology) Journal. 1:121-133. 2007
- High frequency of mutations that expand the host range of an RNA virus. Genetics. 176:1013-1022. 2007
- Ordered vs. unordered samples: response to Bromaghin. Molecular Ecology. 16:4885-4885. 2007
- Stability of a promiscuous plasmid in different hosts: no guarantee for a long-term relationship. Microbiology. 153:452-463. 2007
- Testing the Extreme Value Domain of Attraction for Distributions of Beneficial Fitness Effects. Genetics. 176:2441-2449. 2007
- The population biology of bacterial plasmids: A hidden Markov model approach. Genetics. 176:957-968. 2007
- Markov Chain Monte Carlo in small worlds. Statistics and Computing. 16:193-202. 2006
- Comments on 'Bayesian hierarchical error model for analysis of gene expression data'. Bioinformatics. 22:2446-2451. 2006
- Phylogeography and mitochondrial diversity of extirpated brown bear (Ursus arctos) populations in the contiguous United States and Mexico. Molecular Ecology. 15:4477-4485. 2006
- Properties of adaptive walks on uncorrelated landscapes under strong selection and weak mutation. Journal of Theoretical Biology. 243:114-120. 2006
- Statistical methods for characterizing diversity of microbial communities by analysis of terminal restriction fragment length polymorphisms of 16S rRNA genes. Environmental Microbiology. 8:929-938. 2006
- 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. 2005
- A new method for estimating the size of small populations from genetic mark-recapture data. Molecular Ecology. 14:1991-2005. 2005
- An Empirical Test of The Mutational Landscape Model of Adaptation Using A Single-stranded Dna Virus. Nature Genetics. 37:441-444. 2005
- Evaluating the performance of a successive-approximations approach to parameter optimization in maximum-likelihood phylogeny estimation. Molecular Biology and Evolution. 22:1386-1392. 2005
- Model selection in phylogenetics. Annual Review of Ecology Evolution and Systematics. 36:445-466. 2005
- Modeling the impact of periodic bottlenecks, unidirectional mutation, and observational error in experimental evolution.. Journal of Mathematical Biology. 50:645-662. 2005
- Testing population genetic structure using parametric bootstrapping and MIGRATE-N. Genetica. 124:71-75. 2005
- Use of stochastic models to assess the effect of environmental factors on microbial growth. Applied and Environmental Microbiology. 71:2355-2364. 2005
- 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. 168:1131-1144. 2004
- Evaluating the performance of likelihood methods for detecting population structure and migration. Molecular Ecology. 13:837-851. 2004
- Performance-based selection of likelihood models for phylogeny estimation. Systematic Biology. 52:674-683. 2003
- When can one detect overdominant selection in the infinite-alleles model?. Annals of Applied Probability. 13:181-212. 2003
- Assessing allelic dropout and genotype reliability using maximum likelihood. Genetics. 160:357-366. 2002
- Gaussian limits associated with the Poisson-Dirichlet distribution and the Ewens sampling formula. Annals of Applied Probability. 12:101-124. 2002
- Efficient use of animal manure on cropland - economic analysis. Bioresource Technology. 79:179-191. 2001
- The power to detect recombination using the coalescent. Molecular Biology and Evolution. 18:1421-1424. 2001
- Likelihoods and simulation methods for a class of nonneutral population genetics models. Genetics. 159:853-867. 2001
- NoBLUE among phylogenetic estimators. Journal of Mathematical Biology. 39:421-438. 1999
- Partition structures and sufficient statistics. Journal of Applied Probability. 35:622-632. 1998
- Effect of anionic salts in prepartum diets based on alfalfa. Journal of Dairy Science. 80:2866-2875. 1997
- Robustness of the Ewens sampling formula. Journal of Applied Probability. 32:609-622. 1995
- The distribution of rare alleles. Journal of Mathematical Biology. 33:602-618. 1995
- Likelihood ratios for the infinite alleles model. Journal of Applied Probability. 31:595-605. 1994
- Poisson limit laws for dependent random permutations. Advances In Applied Probability. 24:775-775. 1992
- Weak-convergence of population genealogical processes to the coalescent with ages. Annals of Probability. 20:322-341. 1992
- Consistent ordered sampling distributions. Advances In Applied Probability. 23:229-258. 1991
- Estimating the frequency of the oldest allele, a Bayesian approach. Advances In Applied Probability. 23:456-475. 1991
- Random permutations and neutral evolution models. Stochastic Processes and their Applications. 36:245-261. 1990
- Is knowing the age-order of alleles in a sample useful in testing for selective neutrality?. Genetics. 122:705-711. 1989
- Continuity and weak convergence of ranked and size-biased permutations. Stochastic Processes and their Applications. 31:9-103. 1989
- Cycles, permutations and the structure of the Yule process with immigration. Stochastic Processes and their Applications. 25:89-103. 1987
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chapter
- Practical implications of coalescent theory. Problem Solving Handbook in Computational Biology and Bioinformatics. 63-84. 2011
- Linear estimators for the evolution of transposable elements. Statistics in Molecular Biology and Genetics. 207-220. 1999
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software