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- A chromosome-scale assembly of the axolotl genome. Smith JJ*, Timoshevskaya N, Timoshevskiy VA, Keinath MC, Hardy D, Voss SR (2019) Genome Research, 29: 317-324.
- The Sea Lamprey Germline Genome Provides Insights Into Programmed Genome Rearrangement and Vertebrate Evolution. Smith JJ*, Timoshevskaya N, Ye C, Holt C, Keinath MC, Parker HJ, Cook ME, Hess JE, Narum SR, Lamanna F, Kaessmann H, Timoshevskiy VA, Waterbury CKM, Saraceno C, Wiedemann LM, Robb SMC, Baker C, Eichler EE, Hockman D, Sauka-Spengler T, Yandell M, Krumlauf R, Elgar G, Amemiya CT (2018) Nature Genetics, 50:270-277.
- Deep Ancestry of Programmed Genome Rearrangement in Lampreys. Timoshevskiy VA, Lampman RT, Hess JE, Porter LE, Smith JJ* (2017) Developmental Biology, 429:31-34.
- Cellular and molecular features of developmentally programmed genome rearrangement in a vertebrate (sea lamprey: Petromyzon marinus). Timoshevskiy VA, Herdy JR, Keinath MC, Smith JJ* (2016) PLoS Genetics, 12:e1006103.
- Initial characterization of the large genome of the salamander Ambystoma mexicanum using shotgun and laser capture chromosome sequencing. Keinath MC, Timoshevskaya, NY, Timoshevskiy VA, Tsonis PA, Voss SR, Smith JJ* (2015) Scientific Reports, 5:16413.
- The sea lamprey meiotic map improves resolution of ancient vertebrate genome duplications. Smith JJ, Keinath MC (2015) Genome Research, 25:1081-1090.
- Sequencing of the sea lamprey (Petromyzon marinus) genome provides insights into vertebrate evolution. Smith JJ, Kuraku S, Holt C, Sauka-Spengler T, Jiang N, Campbell MS, Yandell MD, Manousaki T, Meyer A, Bloom OE, Morgan JR, Buxbaum JD, Sachidanandam R, Sims C, Garruss AS, Cook M, Krumlauf R, Wiedemann LM, Sower SA, Decatur WA, Hall JA, Amemiya CT, Saha NR, Buckley KM, Rast JP, Das S, Hirano M, McCurley N, Guo P, Rohner N, Tabin CJ, Piccinelli P, Elgar G, Ruffier M, Aken BL, Searle SMJ, Muffato M, Pignatelli M, Herrero J, Jones M, Brown CT, Chung-Davidson YW, Nanlohy KG, Libants SV, Yeh CY, McCauley DW, Langeland JA, Pancer Z, Fritzsch B, de Jong PJ, Zhu B, Fulton LL, Theising B, Flicek P, Bronner M, Warren WC, Clifton SW, Wilson RK, Li W. (2013) Nature Genetics, 45:415-421.
- Genetic consequences of programmed genome rearrangement. Smith JJ, Baker C, Eichler EE, Amemiya CT (2012). Current Biology 22:1524-1529.