Smith, J., Sumiyama, K., & Amemiya, C. (2012). A living fossil in the genome of a living fossil: Harbinger transposons in the coelacanth genome. Molecular Biology and Evolution, 29(3), 985-93. https://doi.org/10.1093/molbev/msr267

Smith, J., Saha, N., & Amemiya, C. (2010). Genome biology of the cyclostomes and insights into the evolutionary biology of vertebrate genomes. Integrative and Comparative Biology, 50(1), 130-7. https://doi.org/10.1093/icb/icq023

Smith, J., Stuart, A., Sauka-Spengler, T., Clifton, S., & Amemiya, C. (2010). Development and analysis of a germline BAC resource for the sea lamprey, a vertebrate that undergoes substantial chromatin diminution. Chromosoma, 119(4), 381-9. https://doi.org/10.1007/s00412-010-0263-z

Smith, J., Antonacci, F., Eichler, E., & Amemiya, C. (2009). Programmed loss of millions of base pairs from a vertebrate genome. Proceedings of the National Academy of Sciences of the United States of America, 106(27), 11212-7. https://doi.org/10.1073/pnas.0902358106 (Original work published 2009)

Smith, J., Baker, C., Eichler, E., & Amemiya, C. (2012). Genetic consequences of programmed genome rearrangement. Current Biology : CB, 22(16), 1524-9. https://doi.org/10.1016/j.cub.2012.06.028 (Original work published 2012)

Smith, J., Kuraku, S., Holt, C., Sauka-Spengler, T., Jiang, N., Campbell, M., … Li, W. (2013). Sequencing of the sea lamprey (Petromyzon marinus) genome provides insights into vertebrate evolution. Nature Genetics, 45(4), 415-21, 421e1. https://doi.org/10.1038/ng.2568

Amemiya, C., Alföldi, J., Lee, A., Fan, S., Philippe, H., Maccallum, I., … Lindblad-Toh, K. (2013). The African coelacanth genome provides insights into tetrapod evolution. Nature, 496(7445), 311-6. https://doi.org/10.1038/nature12027 (Original work published 2013)

Braasch, I., Gehrke, A., Smith, J., Kawasaki, K., Manousaki, T., Pasquier, J., … Postlethwait, J. (2016). The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons. Nature Genetics, 48(4), 427-37. https://doi.org/10.1038/ng.3526

Bryant, S., , Amemiya, C., & Smith, J. (2016). Characterization of Somatically-Eliminated Genes During Development of the Sea Lamprey (Petromyzon marinus). Molecular Biology and Evolution, 33(9), 2337-44. https://doi.org/10.1093/molbev/msw104

Smith, J., Timoshevskaya, N., Ye, C., Holt, C., Keinath, M., Parker, H., … Amemiya, C. (2018). The sea lamprey germline genome provides insights into programmed genome rearrangement and vertebrate evolution. Nature Genetics, 50(2), 270-277. https://doi.org/10.1038/s41588-017-0036-1