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Preprints

Wolfe, A. D., P. D. Blischak, and L. S. Kubatko. 2021. Phylogenetics of a rapid, continental radiation: Diversification, biogeography, and circumscription of the Beardtongues (Penstemon; Plantaginaceae). [preprint]


Peer-Reviewed Articles

Blischak, P. D., M. Sajan\(^{\ddagger}\), M. S. Barker, R. N. Gutenkunst. In press. Demographic History Inference and the Polyploid Continuum. Genetics. \(^{\ddagger}\)Undergraduate researcher. [link :: preprint :: GitHub]

Blischak, P. D., M. S. Barker, and R. N. Gutenkunst. 2021. Chromosome-scale inference of hybrid speciation and admixture with convolutional neural networks. Molecular Ecology Resources 21:2676–2688. [link :: preprint :: GitHub]

Kang, L., L. Qian, M. Zheng, L. Chen, H. Chen, L. Yang, L. You, B. Yang, M. Yan, Y. Gu, T. Wang, S.-V. Schiessl, H. An, P. D. Blischak, X. Liu, H. Lu, D. Zhang, Y. Rao, D. Jia, D. Zhou, H. Xiao, Y. Wang, X. Xiong, A. S. Mason, J. C. Pires, R. J. Snowdon, W. Hua, and Z. Liu. 2021. Genomic insights into the origin, domestication and diversification of Brassica juncea. Nature Genetics 53:1392–1402. [link]

Li, Z., M. T. W. McKibben, G. S. Finch, P. D. Blischak, B. L. Sutherland, and M. S. Barker. 2021. Patterns and processes of diploidization in land plants. Annual Review of Plant Biology 72:387–410. [link :: preprint]

Qi, X., H. An, T. E. Hall, C. Di, P. D. Blischak, M. T. W. McKibben, Y. Hao, G. C. Conant, J. C. Pires, and M. S. Barker. 2021. Genes derived from ancient polyploidy have higher genetic diversity and are associated with domestication in Brassica rapa. New Phytologist 230:372–386. [link :: preprint]

Mabry, M. E., J. M. Brose, P. D. Blischak, B. Sutherland, W. T. Dismukes, C. A. Bottoms, P. P. Edger, J. D. Washburn, H. An, J. C. Hall, M. R. McKain, I. Al-Shehbaz, M. S. Barker, M. E. Schranz, G. C. Conant, and J. C. Pires. 2020. Phylogeny and multiple independent whole-genome duplication events in the Brassicales. American Journal of Botany 107:1148–1164. [link :: preprint]

Blischak, P. D., M. S. Barker, and R. N. Gutenkunst. 2020. Inferring the demographic history of inbred species from genome-wide SNP frequency data. Molecular Biology and Evolution 37:2124–2136. [link :: preprint :: GitHub]

Grindstaff, B.\(^{\ddagger}\), M. E. Mabry, P. D. Blischak, M. Quinn, and J. C. Pires. 2019. Affordable remote monitoring of plant growth and facilities using Raspberry Pi computers. Applications in Plant Sciences 7:e11280. \(^{\ddagger}\)Undergraduate author. [link :: preprint :: GitHub]

Titus, B. M., P. D. Blischak, and M. Daly. 2019. Genomic signatures of sympatric speciation with historical and contemporary gene flow in a tropical anthozoan. Molecular Ecology 28:3572–3586. [link :: preprint :: GitHub]

Blischak, P. D.*, M. E. Mabry*, G. C. Conant, and J. C. Pires. 2018. Integrating networks, phylogenomics, and population genomics for the study of polyploidy. Annual Review of Ecology, Evolution, and Systematics 49:253–278. *Co-first authors. [link]

Blischak, P. D., J. Chifman, A. D. Wolfe, and L. S. Kubatko. 2018. HyDe: a Python package for genome-scale hybridization detection. Systematic Biology 67:821–829. [link :: preprint :: GitHub]

Blischak, P. D., M. Latvis, D. F. Morales-Briones, J. C. Johnson, V. S. Di Stilio, A. D. Wolfe, and D. C. Tank. 2018. Fluidigm2PURC: automated processing and haplotype inference for double-barcoded PCR amplicons. Applications in Plant Sciences 6:e1156. [link :: preprint :: GitHub :: Docker]

Blischak, P. D., L. S. Kubatko, and A. D. Wolfe. 2018. SNP genotyping and parameter estimation in polyploids using low-coverage sequencing data. Bioinformatics 34:407–415. [link :: preprint :: GitHub]

Latvis, M., S. J. Jacobs, S. M. E. Mortimer, M. Richards, P. D. Blischak, S. Mathews, and D. C. Tank. 2017. Primers for Castilleja and their utility across Orobanchaceae: II. single-copy nuclear loci. Applications in Plant Sciences 5:1700038. [link]

Wolfe, A. D., T. Necamp, S. Fassnacht, P. D. Blischak, and L. S. Kubatko. 2016. Population genetics of Penstemon albomarginatus (Plantaginaceae), a rare Mojave Desert species of conservation concern. Conservation Genetics 17:1245–1255. [link]

Blischak, P. D., L. S. Kubatko, and A. D. Wolfe. 2016. Accounting for genotype uncertainty in the estimation of allele frequencies in autopolyploids. Molecular Ecology Resources 16:742–754. [link :: preprint :: Dryad :: GitHub]

Blischak, P. D., A. J. Wenzel, and A. D. Wolfe. 2014. Gene prediction and annotation in Penstemon (Plantaginaceae): a workflow for marker development from extremely low-coverage genome sequencing. Applications in Plant Sciences 2:1400044. [link :: Dryad]

Book Chapters

Blischak, P. D., C. E. Thompson, E. M. Waight, L. S. Kubatko, and A. D. Wolfe. 2023. “Inferring patterns of hybridization and polyploidy in the plant genus Penstemon (Plantaginaceae).” In L. S. Kubatko and L. Lacey Knowles (ed.), Species Tree Inference: A Guide to Methods and Applications, Princeton University Press, pp. 175–190. [preprint]