selected publications
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academic article
- Ecological Approach to Understanding Superinfection Inhibition in Bacteriophage. Viruses. 13:1389. 2021
- Phi X174 Attenuation by Whole-Genome Codon Deoptimization. Genome Biology and Evolution. 13. 2021
- ΦX174 Attenuation by Whole Genome Codon Deoptimization. Genome Biology and Evolution. 2020
- Saturation Mutagenesis Genome Engineering of Infective PhiX174 Bacteriophage via Unamplified Oligo Pools and Golden Gate Assembly. ACS Synthetic Biology. 2020
- Tracing the history of LINE and SINE extinction in sigmodontine rodents. Mobile DNA. 10:22. 2019
- Selecting among three basic fitness landscape models: Additive, multiplicative and stickbreaking. Theoretical Population Biology. 122:97-109. 2018
- 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
- Integration of molecular cytogenetics, dated molecular phylogeny, and model-based predictions to understand the extreme chromosome reorganization in the Neotropical genus Tonatia (Chiroptera: Phyllostomidae). Bmc Evolutionary Biology. 15. 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
- Selection Affects Genes Involved in Replication during Long-Term Evolution in Experimental Populations of the Bacteriophage phi X174. PLOS One. 8. 2013
- 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
- Retrofitting The Genome: L1 Extinction Follows Endogenous Retroviral Expansion In A Group of Muroid Rodents. Journal of Virology. 85:12315-12323. 2011
- Experimental evolution of viruses: Microviridae as a model system. Philosophical Transactions of the Royal Society B: Biological Sciences. 365:2495-2501. 2010
- Viral Adaptation to an Antiviral Protein Enhances the Fitness Level to above that of the Uninhibited Wild Type. Journal of Virology. 83:11746-11750. 2009
- X Chromosome Inactivation and Xist Evolution in a Rodent Lacking LINE-1 Activity. PLOS One. 4. 2009
- Space, Time, and Host Evolution Facilitate Coexistence of Competing Bacteriophages: Theory and Experiment. American Naturalist. 173:E121-E138. 2009
- Genic Incompatibilities In Two Hybrid Bacteriophages. Molecular Biology and Evolution. 26:2831-2839. 2009
- The Genetics of Adaptation For Eight Microvirid Bacteriophages. Journal of Molecular Evolution. 69:229-239. 2009
- Beneficial Fitness Effects Are Not Exponential For Two Viruses. Journal of Molecular Evolution. 67:368-376. 2008
- Experimental Evolution and Genome Sequencing Reveal Variation In Levels of Clonal Interference In Large Populations of Bacteriophage Phi X174. Bmc Evolutionary Biology. 8. 2008
- Loss of LINE-1 activity in the megabats. Genetics. 178:393-404. 2008
- Testing the Extreme Value Domain of Attraction for Distributions of Beneficial Fitness Effects. Genetics. 176:2441-2449. 2007
- Variable Epistatic Effects Between Mutations at Host Recognition Sites in Phi X174 Bacteriophage. Evolution. 61:1710-1724. 2007
- Evolutionary Feedback Mediated Through Population Density, Illustrated With Viruses In Chemostats. American Naturalist. 167:E39-E51. 2006
- X Accumulation of LINE-1 Retrotransposons in Tokudaia Osimensis, a Spiny Rat with the Karyotype Xo. Cytogenetic and Genome Research. 112:261-269. 2006
- Horizontal Gene Transfer and The Evolution of Microvirid Coliphage Genomes. Journal of Bacteriology. 188:1134-1142. 2006
- Variable Pleiotropic Effects From Mutations at The Same Locus Hamper Prediction of Fitness From a Fitness Component. Genetics. 172:2047-2056. 2006
- Adaptive Molecular Evolution For 13,000 Phage Generations: A Possible Arms Race. Genetics. 170:19-31. 2005
- An Empirical Test of The Mutational Landscape Model of Adaptation Using A Single-stranded Dna Virus. Nature Genetics. 37:441-444. 2005
- Extinction of Line-1 Activity Coincident With A Major Mammalian Radiation In Rodents. Cytogenetic and Genome Research. 110:407-415. 2005
- Mystr: An Endogenous Retrovirus Family In Mammals That Is Undergoing Recent Amplifications To Unprecedented Copy Numbers. Journal of Virology. 79:14698-14707. 2005
- SINE Extinction Preceded LINE Extinction In Sigmodontine Rodents: Implications For Retrotranspositional Dynamics and Mechanisms. Cytogenetic and Genome Research. 110:416-425. 2005
- An Ancient Retrovirus-like Element Contains Hot Spots For Sine Insertion. Genetics. 158:769-777. 2001
- Applied Evolution. Annual Review of Ecology and Systematics. 32:183-217. 2001
- Experimental Evolution Recapitulates Natural Evolution. Philosophical Transactions of the Royal Society B: Biological Sciences. 355:1677-1684. 2000
- Big-benefit Mutations In a Bacteriophage Inhibited With Heat. Molecular Biology and Evolution. 17:942-950. 2000
- The End of the LINE?: Lack of Recent L1 Activity in a Group of South American Rodents. Genetics. 154:1809-1817. 2000
- Evolutionary Reversals During Viral Adaptation To Alternating Hosts. Genetics. 154:27-37. 2000
- Isolation of Markers From Recently Transposed Line-1 Retrotransposons. BioTechniques. 29:1310-1310. 2000
- Different Trajectories of Parallel Evolution During Viral Adaptation. Science (New York, N.Y). 285:422-424. 1999
- Effects of Domestication On Telomere Length In Mus Musculus and Peromyscus Maniculatus. FASEB Journal. 12:A317-A317. 1998
- Molecular Evolution of Two Lineages of L1 (line-1) Retrotransposons In The California Mouse, Peromyscus Californicus. Genetics. 150:345-357. 1998
- Exceptional Convergent Evolution In a Virus. Genetics. 147:1497-1507. 1997
- Analysis of Orthologous Retrovirus-like Elements In The White-footed Mouse, Peromyscus Leucopus. Journal of Molecular Evolution. 44:74-80. 1997
- Computer simulation of transposable element evolution: random template and strict master models. Journal of Molecular Evolution. 42:52-58. 1996
- Retrotransposon Mys Was Active During Evolution of The Peromyscus Leucopus-maniculatus Complex. Journal of Molecular Evolution. 42:44-51. 1996
- Two Persistent LINE-1 Lineages In Peromyscus Have Unequal Rates of Evolution. Genetics. 142:1289-1298. 1996
- Unusual Pattern of Bacterial Ice Nucleation Gene Evolution. Molecular Biology and Evolution. 11:911-920. 1994
- Rapidly Evolving Repetitive Dnas In A Conservative Genome: A Test of Factors That Affect Chromosomal Evolution. Chromosome Research. 2:354-360. 1994
- Genome Organization of Repetitive Elements In The Rodent, Peromyscus-leucopus. Mammalian Genome. 4:374-381. 1993
- Molecular Phylogenetics of Stenodermatini Bat Genera - Congruence of Data From Nuclear and Mitochondrial-DNA. Molecular Biology and Evolution. 10:944-959. 1993
- Restriction Fragment Length Polymorphisms In Satellite Dna Distinguish Chromosomal Races of The White-footed Mouse Peromyscus Leucopus. Molecular Ecology. 1:251-254. 1992
- In Search of Retrotransposons - Exploring The Potential of The Pcr. BioTechniques. 13:258-258. 1992
- Intragenomic Movement and Concerted Evolution of Satellite Dna In Peromyscus - Evidence From Insitu Hybridization. Cytogenetics and Cell Genetics. 60:40-40. 1992
- Transposable Elements and the Evolution of Genome Organization in Mammals. Genetica. 86:287-293. 1992
- Genomic Distribution of Heterochromatic Sequences In Equids - Implications To Rapid Chromosomal Evolution. Journal of Heredity. 82:369-377. 1991
- Genetic-variation For Seasonal Adaptation In Peromyscus-leucopus - Nonreciprocal Breakdown In A Population Cross. Journal of Heredity. 84:89-89. 1991
- Retrotransposon Mys Is Concentrated On The Sex-chromosomes - Implications For Copy Number Containment. Evolution. 44:2083-2088. 1990
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article
- Obituary: Paul Joyce (1958-2016). Biology Letters. 12. 2016
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book section
- Molecular Approaches To Mammalian Retrotransposon Isolation. Ed. 224. 1993
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chapter
- Linear estimators for the evolution of transposable elements. Statistics in Molecular Biology and Genetics. 207-220. 1999
- Molecular approaches to mammalian retrotransposon isolation. Methods in Enzymology. 309-322. 1993
- Transposable elements and the evolution of genome organization in mammals. Transposable elements and the evolution of genome organization in mammals. 149-155. 1993
- Intrageneric variation in repetitive sequences isolated by phylogenetic screening of mammalian genomes. Molecular Evolution. 153-160. 1990
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conference paper
- Natural science databases: resource management and public health. Organization of Fish and Wildlife Information Managers: Proceedings of the 4th Annual Conference. 10-20. 1996
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editorial article
- A revolution in evolution. Science (New York, N.Y). 1998. 1998