Philip L Johnson

Philip L F Johnson

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Philip L Johnson

Philip L F Johnson

Publications by authors named "Philip L F Johnson"

28Publications

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1PubMed Central Citations

Visualization and prediction of CRISPR incidence in microbial trait-space to identify drivers of antiviral immune strategy.

ISME J 2019 Oct 25;13(10):2589-2602. Epub 2019 Jun 25.

Department of Biology, University of Maryland, College Park, MD, USA.

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http://dx.doi.org/10.1038/s41396-019-0411-2DOI Listing
October 2019

Selective Maintenance of Multiple CRISPR Arrays Across Prokaryotes.

CRISPR J 2018 12;1:405-413

Department of Biology, University of Maryland College Park , College Park, Maryland.

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http://dx.doi.org/10.1089/crispr.2018.0034DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6342168PMC
December 2018

Immune loss as a driver of coexistence during host-phage coevolution.

ISME J 2018 02 12;12(2):585-597. Epub 2018 Jan 12.

Department of Biology, University of Maryland College Park, College Park, MD, USA.

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http://dx.doi.org/10.1038/ismej.2017.194DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5776473PMC
February 2018

mapDamage2.0: fast approximate Bayesian estimates of ancient DNA damage parameters.

Bioinformatics 2013 Jul 23;29(13):1682-4. Epub 2013 Apr 23.

Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 København K, Denmark.

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http://dx.doi.org/10.1093/bioinformatics/btt193DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3694634PMC
July 2013

Peripheral selection rather than thymic involution explains sudden contraction in naive CD4 T-cell diversity with age.

Proc Natl Acad Sci U S A 2012 Dec 10;109(52):21432-7. Epub 2012 Dec 10.

Department of Biology, Emory University, Atlanta, GA 30322, USA.

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http://www.pnas.org/cgi/doi/10.1073/pnas.1209283110
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http://dx.doi.org/10.1073/pnas.1209283110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3535632PMC
December 2012

Mutation rate distribution inferred from coincident SNPs and coincident substitutions.

Genome Biol Evol 2011 13;3:842-50. Epub 2011 May 13.

Department of Biology, Emory University, Atlanta, Georgia, USA.

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http://dx.doi.org/10.1093/gbe/evr044DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3172574PMC
December 2011

Inference of microbial recombination rates from metagenomic data.

PLoS Genet 2009 Oct 2;5(10):e1000674. Epub 2009 Oct 2.

Biophysics Graduate Group, University of California Berkeley, Berkeley, California, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1000674DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2745702PMC
October 2009

Accounting for bias from sequencing error in population genetic estimates.

Mol Biol Evol 2008 Jan 2;25(1):199-206. Epub 2007 Nov 2.

Biophysics Graduate Group, University of California, Berkeley, USA.

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http://dx.doi.org/10.1093/molbev/msm239DOI Listing
January 2008

Patterns of damage in genomic DNA sequences from a Neandertal.

Proc Natl Acad Sci U S A 2007 Sep 21;104(37):14616-21. Epub 2007 Aug 21.

Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103 Leipzig, Germany.

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http://dx.doi.org/10.1073/pnas.0704665104DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1976210PMC
September 2007

Utility of R0 as a predictor of disease invasion in structured populations.

J R Soc Interface 2007 Apr;4(13):315-24

Northern Rocky Mountain Science Centre, US Geological Survey, Montana State University, Bozeman, MT 59717, USA.

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http://dx.doi.org/10.1098/rsif.2006.0185DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2359845PMC
April 2007

Inference of population genetic parameters in metagenomics: a clean look at messy data.

Genome Res 2006 Oct 5;16(10):1320-7. Epub 2006 Sep 5.

Biophysics Graduate Group, University of California, Berkeley, California 94720, USA.

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http://dx.doi.org/10.1101/gr.5431206DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1581441PMC
October 2006

Nucleotides of transcription factor binding sites exert interdependent effects on the binding affinities of transcription factors.

Nucleic Acids Res 2002 Mar;30(5):1255-61

Harvard University Graduate Biophysics Program, Harvard Medical School, Boston, MA 02115, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC101241PMC
http://dx.doi.org/10.1093/nar/30.5.1255DOI Listing
March 2002