- Inference of population genetic parameters in metagenomics: a clean look at messy dataPhilip L F Johnson
Biophysics Graduate Group, University of California, Berkeley, California 94720, USA
Genome Res 16:1320-7. 2006..We illustrate the use of our technique on a new project analyzing activated sludge from a lab-scale bioreactor seeded by a wastewater treatment plant...
- Accounting for bias from sequencing error in population genetic estimatesPhilip L F Johnson
Biophysics Graduate Group, University of California, Berkeley, USA
Mol Biol Evol 25:199-206. 2008..We propose a rule of thumb to judge when a given threshold will lead to significant bias and suggest alternative approaches that reduce bias...
- Inference of microbial recombination rates from metagenomic dataPhilip L F Johnson
Biophysics Graduate Group, University of California Berkeley, Berkeley, California, United States of America
PLoS Genet 5:e1000674. 2009..The method itself makes no assumption specific to microbial populations, opening the door for application to any mixed population sample where the number of individuals sampled is much greater than the number of fragments sequenced...
- Patterns of damage in genomic DNA sequences from a NeandertalAdrian W Briggs
Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D 04103 Leipzig, Germany
Proc Natl Acad Sci U S A 104:14616-21. 2007..The results suggest that reliable genome sequences can be obtained from Pleistocene organisms...
- A complete Neandertal mitochondrial genome sequence determined by high-throughput sequencingRichard E Green
Max Planck Institute for Evolutionary Anthropology, D 04103 Leipzig, Germany
Cell 134:416-26. 2008..There is evidence that purifying selection in the Neandertal mtDNA was reduced compared with other primate lineages, suggesting that the effective population size of Neandertals was small...