Philip Johnson
Contact Info
Phone: 301.405.6176
Office: 2207 Biology-Psychology Bldg
Philip Johnson
Associate Professor

Graduate Program Affiliations

  • BISI-Computational Biology, Bioinformatics and Genomics (CBBG)
  • BISI-Behavior, Ecology, Evolution, and Systematics (BEES)

Research Interests

We develop statistical and mathematical models to make sense of large-scale population genomic data at multiple levels.  New types of data from collaborators inspire new types of theory and vice versa.  Population genetics provides an incredible tool to uncover the past to infer the key times and places at which natural selection acted or demography changed.

Specific research projects involve:

  • Interrogating the dynamics of the adaptive immune system through the lens of evolution, whereby the diversity of T cell repertoire in a single individual evolves on both short timescales (during and shortly after infections/vaccinations) and long timescales (during aging).
  • Inferring the presence of contamination and damage in ancient DNA.
  • Understanding mutation rate evolution, particularly in the hominid phylogeny.


Ph.D., Biophysics with a Designated Emphasis in Computational & Genomic Biology, UC Berkeley, 2009
A.B., Harvard College, 2001

All Publications

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Latest Publications via PubMed

Xiao W,Weissman JL,Johnson PLF
bioRxiv. 2024 May 16;:. pii: 2024.05.16.594560. doi: 10.1101/2024.05.16.594560. Epub 2024 May 16
Rasband SA,Bolton PE,Fang Q,Johnson PLF,Braun MJ
Genome Biol Evol. 2023 Mar 3;15(3):. doi: 10.1093/gbe/evad033. Epub
Johnson PLF,Bergstrom CT,Regoes RR,Longini IM,Halloran ME,Antia R
Lancet. 2022 Oct 8;400(10359):1191-1193. doi: 10.1016/S0140-6736(22)01789-5. Epub 2022 Sep 21
Whittier CA,Nutter FB,Johnson PLF,Cross P,Lloyd-Smith JO,Slenning BD,Stoskopf MK
Am J Primatol. 2022 May;84(4-5):e23350. doi: 10.1002/ajp.23350. Epub 2021 Dec 8
Zarnitsyna VI,Akondy RS,Ahmed H,McGuire DJ,Zarnitsyn VG,Moore M,Johnson PLF,Ahmed R,Li KW,Hellerstein MK,Antia R
PLoS Comput Biol. 2021 Oct;17(10):e1009468. doi: 10.1371/journal.pcbi.1009468. Epub 2021 Oct 14
Weissman JL,Dogra S,Javadi K,Bolten S,Flint R,Davati C,Beattie J,Dixit K,Peesay T,Awan S,Thielen P,Breitwieser F,Johnson PLF,Karig D,Fagan WF,Bewick S
BMC Bioinformatics. 2021 Jun 7;22(1):306. doi: 10.1186/s12859-021-04216-2. Epub 2021 Jun 7
Yiu HH,Schoettle LN,Garcia-Neuer M,Blattman JN,Johnson PLF
Immunology. 2021 Apr;162(4):464-475. doi: 10.1111/imm.13299. Epub 2021 Jan 11
Weissman JL,Stoltzfus A,Westra ER,Johnson PLF
Trends Microbiol. 2020 Jul;28(7):543-553. doi: 10.1016/j.tim.2020.02.005. Epub 2020 Apr 10
Weissman JL,Johnson PLF
mSystems. 2020 Jan 14;5(1):. doi: 10.1128/mSystems.00752-19. Epub 2020 Jan 14
Weissman JL,Fagan WF,Johnson PLF
PLoS Genet. 2019 Nov;15(11):e1008493. doi: 10.1371/journal.pgen.1008493. Epub 2019 Nov 8
Weissman JL,Laljani RMR,Fagan WF,Johnson PLF
ISME J. 2019 Oct;13(10):2589-2602. doi: 10.1038/s41396-019-0411-2. Epub 2019 Jun 25
Weissman JL,Fagan WF,Johnson PLF
CRISPR J. 2018 Dec;1(6):405-413. doi: 10.1089/crispr.2018.0034. Epub
Loreille O,Ratnayake S,Bazinet AL,Stockwell TB,Sommer DD,Rohland N,Mallick S,Johnson PLF,Skoglund P,Onorato AJ,Bergman NH,Reich D,Irwin JA
Genes (Basel). 2018 Mar 1;9(3):. doi: 10.3390/genes9030135. Epub 2018 Mar 1
Weissman JL,Holmes R,Barrangou R,Moineau S,Fagan WF,Levin B,Johnson PLF
ISME J. 2018 Feb;12(2):585-597. doi: 10.1038/ismej.2017.194. Epub 2018 Jan 12