Peer-Reviewed Publications

Polonsky JA, Baidjoe A, Kamvar, ZN Cori A, Durski K, Edmunds WJ, Eggo RM, Funk S, Kaiser L, Keating P, Polain de Waroux O, Marks M, Moraga P, Morgan O, Nouvellet P, Ratnayake R, Roberts CH, Whitworth J, & Jombart T (2019). Outbreak analytics: A developing data science for informing the response to emerging pathogens. Philosophical Transactions of the Royal Society B: Biological Sciences, 374(1776), 20180276. doi: 10.1098/rstb.2018.0276

Kamvar ZN, Cai J, Pulliam JRC, Schumacher J, Jombart T. Epidemic curves made easy using the R package incidence [version 1; peer review: 1 approved, 2 approved with reservations]. F1000Research 2019, 8:139. (doi: 10.12688/f1000research.18002.1).

• software: https://github.com/reconhub/incidence
• doi: 10.5281/zenodo.1404718

Moraga P, Dorigatti I, Kamvar ZN, Piatkowski P, Toikkanen SE, Nagraj V, Donnelly CA, and Jombart T epiflows: an R package for risk assessment of travel-related spread of disease [version 1; referees: 2 approved with reservations]. F1000Research 2018, 7:1374 (doi: 10.12688/f1000research.16032.1)

• software: https://github.com/reconhub/epiflows
• doi: 10.5281/zenodo.1401806

Miorini TJJ, Kamvar ZN, Higgins R, Raetano CG, Steadman JR, Everhart SE. (2018) Variation in pathogen aggression and cultivar performance against Sclerotinia sclerotiorum in soybean and dry bean from Brazil and the U.S. Tropical Plant Pathology doi: 10.1007/s40858-018-00273-w

• data/analysis: https://github.com/everhartlab/SscPhenoProj
  
• doi: 10.17605/OSF.IO/2X7FC

Pannullo A, Kamvar ZN, Miorini TJJ, Steadman JR, Everhart SE. (2018) Genetic variation and structure of Sclerotinia sclerotiorum populations from soybean in Brazil. Tropical Plant Pathology doi: 10.1007/s40858-018-0266-5.

• data/analysis: https://github.com/everhartlab/brazil-sclerotinia-2017
  
• doi: 10.17605/OSF.IO/E4UPH

Kamvar ZN, Everhart SE. (2018) Something in the agar does not compute: on the discriminatory power of mycelial compatibility in Sclerotinia sclerotiorum. Tropical Plant Pathology doi: 10.1007/s40858-018-0263-8
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• simulations: https://github.com/everhartlab/sclerotinia-review-2017
  
• doi: 10.17605/OSF.IO/B8VD3

Kamvar ZN, Amaradasa BS, Jhala R, McCoy S, Steadman JR, Everhart SE. (2017) Population structure and phenotypic variation of Sclerotinia sclerotiorum from dry bean (Phaseolus vulgaris) in the United States. PeerJ 5:e4152 doi: 10.7717/peerj.4152

• data/analysis: https://github.com/everhartlab/sclerotinia-366
  
• doi: 10.17605/OSF.IO/EJB5Y

Grünwald NJ, Everhart SE, Knaus BJ, Kamvar ZN. (2017) Best practices for population genetic analyses. Phytopathology 107:9 doi: 10.1094/PHYTO-12-16-0425-RVW

Jombart T, Archer F, Schliep K, Kamvar ZN, Harris R, Paradis E, Goudet J, Lapp H (2017). apex: phylogenetics with multiple genes. Molecular Ecology Resources. 17:1 19-26 doi: 10.¹¹¹¹⁄₁₇₅₅-0998.12567

Kamvar ZN, López-Uribe MM, Coughlan S, Grünwald NJ, Lapp H, Manel S (2017). Developing educational resources for population genetics in R: an open and collaborative approach. Molecular Ecology Resources. 17:1 120-128 doi: 10.¹¹¹¹⁄₁₇₅₅-0998.12558

Tabima JF, Everhart SE, Larsen MM, Weisberg AJ, Kamvar ZN, Tancos MA, Smart CD, Chang JH, Grünwald NJ. (2016) Microbe-ID: an open source toolbox for microbial genotyping and species identification. PeerJ 4: e2279 doi: 10.7717/peerj.2279

Grünwald NJ, Larsen MM, Kamvar ZN, Reeser PW, Kanaskie A, Laine J, Wiese R (2015) First report of the EU1 clonal lineage of Phytophthora ramorum on tanoak in an OR forest. Plant Disease. 100:5, 1024-1024. doi: 10.1094/PDIS-10-15-1169-PDN

Kamvar ZN, Brooks JC and Grünwald NJ (2015) Novel R tools for analysis of genome-wide population genetic data with emphasis on clonality. Front. Genet. 6: 208. doi: 10.3389/fgene.2015.00208

• data/analysis: https://github.com/grunwaldlab/supplementary-poppr-2.0
  
• doi: 10.5281/zenodo.17424

Kamvar ZN, Larsen MM, Kanaskie AM, Hansen EM, and Grünwald NJ. (2015) Spatial and temporal analysis of populations of the sudden oak death pathogen in Oregon forests. Phytopathology. 105:7 982-989. doi: 10.1094/PHYTO-12-14-0350-FI.

• data/analysis: https://github.com/zkamvar/Sudden_Oak_Death_in_Oregon_Forests
• doi: 10.5281/zenodo.13007

Weiland JE, Garrido PA, Kamvar ZN, Marek SM, Grünwald NJ, and Garzón CD. (2015) Population structure of Pythium irregulare, P. sylvaticum, and P. ultimum in forest nursery soils of Oregon and Washington. Phytopathology. 105:5 684-694. doi: 10.1094/PHYTO-05-14-0147-R

Kamvar ZN, Tabima JF, Grünwald NJ. (2014) Poppr: an R package for genetic analysis of populations with clonal, partially clonal, and/or sexual reproduction. PeerJ 2: e281. doi: 10.7717/peerj.281

Buckner B, Beck J, Browning, K, Hoxha E, Grantham L, Kamvar ZN, Lough A, Nikolova O, and Schnable PS, Scanlon MJ, and Janick-Buckner D. (2007) Involving undergraduates in the annotation and analysis of global gene expression studies: creation of a maize shoot apical meristem expression database. Genetics 176: 741-747. doi: 10.1534/genetics.106.066472