Philip L F Johnson

Graduate student, class of 2004 Slatkin Lab Biophysics Graduate Group University of California, Berkeley

Research interests

1. Population genetics of microbial communities -- to what extent is genetic variation created and maintained? How much genetic material is exchanged between individuals in a community and what effect does this have on their evolution?
2. Sequencing error -- how can we properly account for sequencing error (or ancient DNA degradation, etc.) when making inferences based on population genetic theory?
3. Mathematical disease modelling in structured populations -- how does population structure affect the stochastic initial stages of disease invasion to influence the overall outcome (i.e. pandemic or false alarm)?

Specifically, I am interested in adapting population genetic techniques developed for narrow-but-deep population samples to the wide-but-shallow data produced by metagenomic sequencing projects. In this context, sequencing error can be particularly deceptive because average read depths are low.

The disease modelling interest may intersect population genetics at some point, but this has not happened yet.

Publications

• Johnson PLF, Slatkin M. (2009). Inference of Microbial Recombination Rates from Metagenomic Data. PLoS Genetics, 5(10): e1000674. [doi]
• Green RE, Malaspinas AS, Krause J, Briggs AW, Johnson PLF, Uhler C, Meyer M, Good JM, Maricic T, Stenzel U, Prüfer K, Siebauer M, Burbano HA, Ronan M, Rothberg JM, Egholm M, Rudan P, Brajković D, Kućan Z, Gusić I, Wikström M, Laakkonen L, Kelso J, Slatkin M, Pääbo S. (2008). A complete neandertal mitochondrial genome sequence determined by high-throughput sequencing. Cell, 134(3), 416-26. [doi]
• Johnson PLF, Slatkin M. (2008). Accounting for bias from sequencing error in population genetic estimates. Mol Biol Evol 25, 199-206. [fulltext, doi]
• Briggs AW, Stenzel U, Johnson PLF, Green RE, Kelso J, Prüfer K, Meyer M, Krause J, Ronan MT, Lachmann M, Pääbo S. (2007). Patterns of damage in genomic DNA sequences from a Neandertal. Proc Natl Acad Sci U S A, 104(37), 14616-21. [doi]
• Cross PC, Johnson PLF, Lloyd-Smith JO, Getz WM. (2007). Utility of R0 as a predictor of disease invasion in structured populations. J R Soc Interface 4, 315-324. [doi]
• Johnson PLF, Slatkin M. (2006). Inference of population genetic parameters in metagenomics: a clean look at messy data. Genome Research 16, 1320-1327. [doi]
• Getz WM, Lloyd-Smith JO, Cross PC, Bar-David S, Johnson PLF, Porco TC, Sánchez MS. (2006). Modeling the invasion and spread of contagious disease in heterogeneous populations. In Feng, Z., Dieckmann, U., Levin, S.A. (Eds.), Disease Evolution: Models, Concepts and Data Analyses, AMS-DIMACS Series, pp. 113-144. American Mathematical Society, Providence, RI.
• Cross PC, Lloyd-Smith JO, Johnson PLF, Getz WM. (2005). Duelling timescales of host movement and disease recovery determine invasion of disease in structured populations. Ecology Letters 8, 587-595. [doi]
• International Human Genome Sequencing Consortium. (2004). Finishing the euchromatic sequence of the human genome. Nature 431, 931-945. [doi]
• Bulyk ML, Johnson PLF, Church GM. (2002). Nucleotides of transcription factor binding sites exert interdependent effects on the binding affinities of transcription factors. Nucleic Acids Research 30, 1255-1261. [pmc]

Software

Useful

Why do so few journals supply bibliography style files? Perhaps these BibTeX styles will be useful to someone else:

Journal	File	Date
Genome Research	genome_research.bst (use with genome_research.sty)	Spring 2006
Molecular Biology & Evolution (MBE)	mbe.bst (use with Natbib)	June 2007

Contact

Updated Oct 2009.