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| Drábková M, Kocot KM, Halanych KM, et al. (2022) Different phylogenomic methods support monophyly of enigmatic 'Mesozoa' (Dicyemida + Orthonectida, Lophotrochozoa). Proceedings. Biological Sciences. 289: 20220683 |
| Li Y, Kocot KM, Tassia MG, et al. (2018) Mitogenomics reveals a novel genetic code in Hemichordata. Genome Biology and Evolution |
| Tassia MG, Cannon JT, Konikoff CE, et al. (2016) The Global Diversity of Hemichordata. Plos One. 11: e0162564 |
| Kocot KM, Struck TH, Merkel J, et al. (2016) Phylogenomics of Lophotrochozoa with consideration of systematic error. Systematic Biology |
| Cannon JT, Kocot KM. (2016) Phylogenomics Using Transcriptome Data. Methods in Molecular Biology (Clifton, N.J.). 1452: 65-80 |
| Cannon JT, Vellutini BC, Smith J, et al. (2016) Xenacoelomorpha is the sister group to Nephrozoa. Nature. 530: 89-93 |
| D'Aniello S, Delroisse J, Valero-Gracia A, et al. (2015) Opsin evolution in the Ambulacraria. Marine Genomics |
| Havird JC, Kocot KM, Brannock PM, et al. (2015) Reconstruction of cyclooxygenase evolution in animals suggests variable, lineage-specific duplications, and homologs with low sequence identity. Journal of Molecular Evolution. 80: 193-208 |
| Cannon JT, Kocot KM, Waits DS, et al. (2014) Phylogenomic resolution of the hemichordate and echinoderm clade. Current Biology : Cb. 24: 2827-32 |
| Cannon JT, Swalla BJ, Halanych KM. (2013) Hemichordate molecular phylogeny reveals a novel cold-water clade of harrimaniid acorn worms. The Biological Bulletin. 225: 194-204 |