selected publications
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academic article
- Searching for a mechanistic description of pairwise epistasis in protein systems. Proteins - Structure, Function, and Bioinformatics. 90:1474-1485. 2022
- Priming With Rhinovirus Protects Mice Against a Lethal Pulmonary Coronavirus Infection. Frontiers in Immunology. 13. 2022
- Effects of trust, risk perception, and health behavior on COVID-19 disease burden: Evidence from a multi-state US survey. PLOS One. 2022
- Mutational Switch-Backs Can Accelerate Evolution of Francisella to a Combination of Ciprofloxacin and Doxycycline. Frontiers in Microbiology. 13. 2022
- Global Composition of the Bacteriophage Community in Honey Bees. Msystems. 7. 2022
- Phi X174 Attenuation by Whole-Genome Codon Deoptimization. Genome Biology and Evolution. 13. 2021
- Rhinovirus Reduces the Severity of Subsequent Respiratory Viral Infections by Interferon-Dependent and -Independent Mechanisms. MSPHERE. 6. 2021
- ΦX174 Attenuation by Whole Genome Codon Deoptimization. Genome Biology and Evolution. 2020
- Risk of Disease and Willingness to Vaccinate in the United States: A Population-based Survey. PLOS Medicine. 17:e1003354. 2020
- Saturation Mutagenesis Genome Engineering of Infective PhiX174 Bacteriophage via Unamplified Oligo Pools and Golden Gate Assembly. ACS Synthetic Biology. 2020
- A two-stage experimental design for dilution assays. Biometrics. 75:1009-1016. 2019
- The treacheries of adaptation.. Science (New York, N.Y). 366:418-419. 2019
- Selecting among three basic fitness landscape models: Additive, multiplicative and stickbreaking. Theoretical Population Biology. 122:97-109. 2018
- Lung epithelial cells have virus-specific and shared gene expression responses to infection by diverse respiratory viruses. PLOS One. 12:e0178408. 2017
- New Perspectives on Ebola Virus Evolution. PLOS One. 11. 2016
- Love the one you're with: replicate viral adaptations converge on the same phenotypic change. PeerJ. 4. 2016
- Initiating a watch list for Ebola virus antibody escape mutations. 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
- Changing Folding and Binding Stability in a Viral Coat Protein: A Comparison between Substitutions Accessible through Mutation and Those Fixed by Natural Selection. PLOS One. 9:e112988. 2014
- Capwire: a R package for estimating population census size from non-invasive genetic sampling. Molecular Ecology Resources. 13:154-157. 2013
- The Consistency of Beneficial Fitness Effects of Mutations across Diverse Genetic Backgrounds. PLOS One. 7:e43864. 2012
- Estimating the Number of One-step Beneficial Mutations. Statistical Applications In Genetics and Molecular Biology. 11. 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
- First-Step Mutations for Adaptation at Elevated Temperature Increase Capsid Stability in a Virus. PLOS One. 6:e25640. 2011
- Epistasis Between Beneficial Mutations and The Phenotype-to-fitness Map For A Ssdna Virus. PLOS Genetics. 7. 2011
- Mutational Effects and Population Dynamics During Viral Adaptation Challenge Current Models. Genetics. 187:185-202. 2011
- Ordered vs. unordered samples: response to Bromaghin. Molecular Ecology. 16:4885-4885. 2007
- Phylogeography and mitochondrial diversity of extirpated brown bear (Ursus arctos) populations in the contiguous United States and Mexico. Molecular Ecology. 15:4477-4485. 2006
- A new method for estimating the size of small populations from genetic mark-recapture data. Molecular Ecology. 14:1991-2005. 2005
- Pedigree-based assignment tests for reversing coyote (Canis latrans) introgression into the wild red wolf (Canis rufus) population. Molecular Ecology. 12:3287-3301. 2003
- The history of effective population size and genetic diversity in the Yellowstone grizzly (Ursus arctos): Implications for conservation. Proceedings of the National Academy of Sciences of the United States of America. 100:4334-4339. 2003
- Microsatellite DNA and recent statistical methods in wildlife conservation management: applications in Apline ibex [Capra ibex (ibex)]. Molecular Ecology. 11:421-436. 2002
- Performance measures for ecosystem management and ecological sustainability. Wildlife Society Technical Report B. 2002
- The Endangered Species Act: Dollars and sense?. BioScience. 52:163-168. 2002
- Assessing allelic dropout and genotype reliability using maximum likelihood. Genetics. 160:357-366. 2002
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article
- Obituary: Paul Joyce (1958-2016). Biology Letters. 12. 2016
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chapter
- Estimation of effective population size in Yellowstone grizzly bears . Conservation and the Genetics of Populations, 2nd Edition. 2012
- Estimation of effective population size in Yellowstone grizzly bears. Conservation and the Genetics of Populations. 2007
- Genetically Effective Sizes of Grizzly Bear Populations. Principles of Conservation Biology, 3rd ed. 2005
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software