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Synonymous but not the same: the causes and consequences of codon bias
Ongoing work to quantify the dynamics of initiation and elongation is as important for understanding natural synonymous variation as it is for designing transgenes in applied contexts.
Reconciling molecular phylogenies with the fossil record
- H. Morlon, T. Parsons, J. Plotkin
- Biology, Environmental ScienceProceedings of the National Academy of Sciences
- 19 September 2011
It is shown that realistic extinction rates and diversity trajectories can be inferred from molecular phylogenies, and it is suggested that most extant cetaceans arose from four recent radiations, with a few additional species arising from clades that have been in decline over the last ∼10 Myr.
Coding-Sequence Determinants of Gene Expression in Escherichia coli
In this analysis, mRNA folding and associated rates of translation initiation play a predominant role in shaping expression levels of individual genes, whereas codon bias influences global translation efficiency and cellular fitness.
The Population Genetics of dN/dS
The expected dN/dS ratio for samples drawn from a single population under selection is studied, and it is found that in this context, dN-dS is relatively insensitive to the selection coefficient.
Seed Dispersal and Spatial Pattern in Tropical Trees
It is demonstrated here that the extent and scale of conspecific spatial aggregation is correlated with the mode of seed dispersal, and this relationship holds for saplings as well as for mature trees.
Species-area curves, spatial aggregation, and habitat specialization in tropical forests.
- J. Plotkin, M. Potts, N. Leslie, N. Manokaran, J. Lafrankie, P. Ashton
- Environmental ScienceJournal of theoretical biology
- 7 November 2000
It is concluded that small-scale phenomena such as dispersal and gap recruitment determine individual tree placement more than adaptation to larger-scale topography.
Improved Ribosome-Footprint and mRNA Measurements Provide Insights into Dynamics and Regulation of Yeast Translation.
Inferring the Dynamics of Diversification: A Coalescent Approach
A novel approach to infer diversification dynamics shows that biodiversity is still expanding but at a slower rate than in the past.
Rate-Limiting Steps in Yeast Protein Translation
Dynamical resonance can account for seasonality of influenza epidemics.
- J. Dushoff, J. Plotkin, S. Levin, D. Earn
- MedicineProceedings of the National Academy of Sciences…
- 30 November 2004
It is shown that the large oscillations in incidence may be caused by undetectably small seasonal changes in the influenza transmission rate that are amplified by dynamical resonance.