Papers Using HybPiper as of August, 2018:

Kusy, Dominik, Michal Motyka, Carmelo Andujar, Matej Bocek, Michal Masek, Katerina Sklenarova, Filip Kokas, Milada Bocakova, Alfried P. Vogler, and Ladislav Bocak. 2018. “Genome Sequencing of Rhinorhipus Lawrence Exposes an Early Branch of the Coleoptera.” Frontiers in Zoology 15 (May): 21.
Li, Fay-Wei, Paul Brouwer, Lorenzo Carretero-Paulet, Shifeng Cheng, Jan de Vries, Pierre-Marc Delaux, Ariana Eily, et al. 2018. “Fern Genomes Elucidate Land Plant Evolution and Cyanobacterial Symbioses.” Nature Plants 4 (7): 460–72.
Villaverde, T. , Pokorny, L. , Olsson, S. , Rincón‐Barrado, M. , Johnson, M. G., Gardner, E. M., Wickett, N. J., Molero, J. , Riina, R. and Sanmartín, I. (2018), Bridging the micro‐ and macroevolutionary levels in phylogenomics: Hyb‐Seq solves relationships from populations to species and above. New Phytol. . doi:10.1111/nph.15312
Wolf, P. G., T. A. Robison, M. G. Johnson, M. A. Sundue, W. L. Testo, and C. J. Rothfels. 2018. Target sequence capture of nuclear‐encoded genes for phylogenetic analysis in ferns. Applications in Plant Sciences 6(5): e1148.
Gernandt, D. S., X. Aguirre Dugua, A. Vázquez‐Lobo, A. Willyard, A. Moreno Letelier, J. A. Pérez de la Rosa, D. Piñero, and A. Liston. 2018. Multi‐locus phylogenetics, lineage sorting, and reticulation in Pinus subsection Australes. American Journal of Botany 105(4): 711–725.
Chau, J. H., W. A. Rahfeldt, and R. G. Olmstead. 2018. Comparison of taxon‐specific versus general locus sets for targeted sequence capture in plant phylogenomics. Applications in Plant Sciences 6(3): e1032.
Wen, J. , Harris, A. , Ickert‐Bond, S. M., Dikow, R. , Wurdack, K. and Zimmer, E. A. (2017), Developing integrative systematics in the informatics and genomic era, and calling for a global Biodiversity Cyberbank. Jnl of Sytematics Evolution, 55: 308-321. doi:10.1111/jse.12270
Peris, D., Pérez‐Torrado, R., Hittinger, C. T., Barrio, E., and Querol, A. (2018) On the origins and industrial applications of Saccharomyces cerevisiae × Saccharomyces kudriavzevii hybrids. Yeast, 35: 51–69. doi: 10.1002/yea.3283.
Vatanparast, M., A. Powell, J. J. Doyle, and A. N. Egan. 2018. Targeting legume loci: A comparison of three methods for target enrichment bait design in Leguminosae phylogenomics. Applications in Plant Sciences 6(3): e1036.
Stubbs, Rebecca L., Ryan A. Folk, Chun-Lei Xiang, Douglas E. Soltis, and Nico Cellinese. 2018. “Pseudo-Parallel Patterns of Disjunctions in an Arctic-Alpine Plant Lineage.” Molecular Phylogenetics and Evolution 123 (February): 88–100.
Peris, David, Roberto Pérez-Torrado, Chris Todd Hittinger, Eladio Barrio, and Amparo Querol. 2017. “On the Origins and Industrial Applications of Saccharomyces Cerevisiae × Saccharomyces Kudriavzevii Hybrids.” Yeast , October. https://doi.org/10.1002/yea.3283.
Medina, Rafael, Matthew Johnson, Yang Liu, Nicholas Wilding, Terry A. Hedderson, Norman Wickett, and Bernard Goffinet. 2017. “Evolutionary Dynamism in Bryophytes: Phylogenomic Inferences Confirm Rapid Radiation in the Moss Family Funariaceae.” Molecular Phylogenetics and Evolution, December. https://doi.org/10.1016/j.ympev.2017.12.002.
Landis, J. B., Soltis, D. E., & Soltis, P. S. (2017). Comparative transcriptomic analysis of the evolution and development of flower size in Saltugilia (Polemoniaceae). BMC Genomics, 18(1). doi:10.1186/s12864-017-3868-2
Crowl, A. A., Myers, C., & Cellinese, N. (2017). Embracing discordance: Phylogenomic analyses provide evidence for allopolyploidy leading to cryptic diversity in a Mediterranean Campanula (Campanulaceae) clade. Evolution, 71(4), 913–922. doi:10.1111/evo.13203