Spokony, R. F., Marroquin, C., & Barton, L. J. (2026). Juvenile hormone degradation enzymes in insect development: Emerging insights from functional genetics. Current Opinion in Insect Science, 101584. https://doi.org/10.1016/j.cois.2026.101584

Luu, T., Ramroop, J. R., Lee, M. K., Kaur, H., McGrail, C. W., Govind, S., & Spokony, R. F. (2025). Juvenile hormone mimics induce a cellular immune response in Drosophila melanogaster. Micropublication Biology, 2025, 10–17912.

Spokony, R., Goyins, K., Siegel, H., Healy, C., Alvarado, I., Jumamyradova, A., Naseem, Y., Ying, J., Soshnev, A. A., & Barton, L. J. (2025). Juvenile hormone degradation enzymes have shared and unique requirements in Drosophila development. https://doi.org/10.1101/2025.06.09.657647

Stanek, T. J., Leung, W., Shaffer, C. D., The Genomics Education Partnership, Kleinschmit, A. J., Mix, J., Starkey, J., Ogden, S., Robic, S., Roman, D., Candler, J., Ellis, K. C., Bugay, M., LaMore, P., Wiltz, Z., Dennis, D., Saville, K. J., Martinez, A. M., Wooley, A., … Ellison, C. E. (2025). Recombination Suppression Drives Expansion of the Drosophila Dot Chromosome. Molecular Biology and Evolution, 42(12), msaf304. https://doi.org/10.1093/molbev/msaf304

Magee, M., & Spokony, R. (2023). Effect of D. melanogaster larval density on pupal size. microPublication Biology, 2023. https://doi.org/10.17912/micropub.biology.000959

Lopatto, D., Rosenwald, A. G., Burgess, R. C., Silver Key, C., Van Stry, M., Wawersik, M., DiAngelo, J. R., Hark, A. T., Skerritt, M., Allen, A. K., Alvarez, C., Anderson, S., Arrigo, C., Arsham, A., Barnard, D., Bedard, J. E. J., Bose, I., Braverman, J. M., Burg, M. G., … Reed, L. K. (2022). Student Attitudes Contribute to the Effectiveness of a Genomics CURE. Journal of Microbiology & Biology Education, 23(2), e00208-21. https://doi.org/10.1128/jmbe.00208-21

Laakso, M. M., Paliulis, L. V., Croonquist, P., Derr, B., Gracheva, E., Hauser, C., Howell, C., Jones, C., Kagey, J. D., Kennell, J., Key, S. C. S., Mistry, H., Robic, S., Sanford, J., Santisteban, M., Small, C., Spokony, R., Stamm, J., Stry, M. V., … Elgin, S. C. R. (2021). An undergraduate bioinformatics curriculum that teaches eukaryotic gene structure. https://doi.org/10.24918/cs.2017.13

Lopatto, D., Rosenwald, A. G., DiAngelo, J. R., Hark, A. T., Skerritt, M., Wawersik, M., Allen, A. K., Alvarez, C., Anderson, S., Arrigo, C., Arsham, A., Barnard, D., Bazinet, C., Bedard, J. E. J., Bose, I., Braverman, J. M., Burg, M. G., Burgess, R. C., Croonquist, P., … Elgin, S. C. R. (2020). Facilitating Growth through Frustration: Using Genomics Research in a Course-Based Undergraduate Research Experience. Journal of Microbiology & Biology Education, 21(1), 21.1.6. https://doi.org/10.1128/jmbe.v21i1.2005

Yalgin, C., Ebrahimi, S., Delandre, C., Yoong, L. F., Akimoto, S., Tran, H., Amikura, R., Spokony, R., Torben-Nielsen, B., White, K. P., & Moore, A. W. (2015). Centrosomin represses dendrite branching by orienting microtubule nucleation. Nature Neuroscience, 18(10), 1437–1445. https://doi.org/10.1038/nn.4099

Arthur, R. K., Ma, L., Slattery, M., Spokony, R. F., Ostapenko, A., Nègre, N., & White, K. P. (2014). Evolution of H3K27me3-marked chromatin is linked to gene expression evolution and to patterns of gene duplication and diversification. Genome Research, 24(7), 1115–1124. https://doi.org/10.1101/gr.162008.113

Boyle, A. P., Araya, C. L., Brdlik, C., Cayting, P., Cheng, C., Cheng, Y., Gardner, K., Hillier, L. W., Janette, J., Jiang, L., Kasper, D., Kawli, T., Kheradpour, P., Kundaje, A., Li, J. J., Ma, L., Niu, W., Rehm, E. J., Rozowsky, J., … Snyder, M. (2014). Comparative analysis of regulatory information and circuits across distant species. Nature, 512(7515), 453–456. https://doi.org/10.1038/nature13668

Chanut-Delalande, H., Hashimoto, Y., Pelissier-Monier, A., Spokony, R., Dib, A., Kondo, T., Bohère, J., Niimi, K., Latapie, Y., Inagaki, S., Dubois, L., Valenti, P., Polesello, C., Kobayashi, S., Moussian, B., White, K. P., Plaza, S., Kageyama, Y., & Payre, F. (2014). Pri peptides are mediators of ecdysone for the temporal control of development. Nature Cell Biology, 16(11), 1035–1044. https://doi.org/10.1038/ncb3052

Slattery, M., Ma, L., Spokony, R. F., Arthur, R. K., Kheradpour, P., Kundaje, A., Nègre, N., Crofts, A., Ptashkin, R., Zieba, J., Ostapenko, A., Suchy, S., Victorsen, A., Jameel, N., Grundstad, A. J., Gao, W., Moran, J. R., Rehm, E. J., Grossman, R. L., … White, K. P. (2014). Diverse patterns of genomic targeting by transcriptional regulators in Drosophila melanogaster. Genome Research, 24(7), 1224–1235. https://doi.org/10.1101/gr.168807.113

Greer, C., Lee, M., Westerhof, M., Milholland, B., Spokony, R., Vijg, J., & Secombe, J. (2013). Myc-dependent genome instability and lifespan in Drosophila. PloS One, 8(9), e74641. https://doi.org/10.1371/journal.pone.0074641

Menoret, D., Santolini, M., Fernandes, I., Spokony, R., Zanet, J., Gonzalez, I., Latapie, Y., Ferrer, P., Rouault, H., White, K. P., Besse, P., Hakim, V., Aerts, S., Payre, F., & Plaza, S. (2013). Genome-wide analyses of Shavenbaby target genes reveals distinct features of enhancer organization. Genome Biology, 14(8), R86. https://doi.org/10.1186/gb-2013-14-8-r86

Jungreis, I., Lin, M. F., Spokony, R., Chan, C. S., Negre, N., Victorsen, A., White, K. P., & Kellis, M. (2011). Evidence of abundant stop codon readthrough in Drosophila and other metazoa. Genome Research, 21(12), 2096–2113. https://doi.org/10.1101/gr.119974.110

Nègre, N., Brown, C. D., Ma, L., Bristow, C. A., Miller, S. W., Wagner, U., Kheradpour, P., Eaton, M. L., Loriaux, P., Sealfon, R., Li, Z., Ishii, H., Spokony, R. F., Chen, J., Hwang, L., Cheng, C., Auburn, R. P., Davis, M. B., Domanus, M., … White, K. P. (2011). A cis-regulatory map of the Drosophila genome. Nature, 471(7339), 527–531. https://doi.org/10.1038/nature09990

modENCODE Consortium, Roy, S., Ernst, J., Kharchenko, P. V., Kheradpour, P., Negre, N., Eaton, M. L., Landolin, J. M., Bristow, C. A., Ma, L., Lin, M. F., Washietl, S., Arshinoff, B. I., Ay, F., Meyer, P. E., Robine, N., Washington, N. L., Di Stefano, L., Berezikov, E., … Kellis, M. (2010). Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science (New York, N.Y.), 330(6012), 1787–1797. https://doi.org/10.1126/science.1198374

Spokony, R. F., & Restifo, L. L. (2009). Broad Complex isoforms have unique distributions during central nervous system metamorphosis in Drosophila melanogaster. The Journal of Comparative Neurology, 517(1), 15–36. https://doi.org/10.1002/cne.22119

Venken, K. J. T., Carlson, J. W., Schulze, K. L., Pan, H., He, Y., Spokony, R., Wan, K. H., Koriabine, M., de Jong, P. J., White, K. P., Bellen, H. J., & Hoskins, R. A. (2009). Versatile P[acman] BAC libraries for transgenesis studies in Drosophila melanogaster. Nature Methods, 6(6), 431–434. https://doi.org/10.1038/nmeth.1331

Spokony, R. F., & Restifo, L. L. (2007). Anciently duplicated Broad Complex exons have distinct temporal functions during tissue morphogenesis. Development Genes and Evolution, 217(7), 499–513. https://doi.org/10.1007/s00427-007-0159-y

Spokony, R. F., Aoki, Y., Saint-Germain, N., Magner-Fink, E., & Saint-Jeannet, J.-P. (2002). The transcription factor Sox9 is required for cranial neural crest development in Xenopus. Development (Cambridge, England), 129(2), 421–432. https://doi.org/10.1242/dev.129.2.421

Spokony, R., & Saint-Jeannet, J. P. (2000). Xenopus FK 506-binding protein, a novel immunophilin expressed during early development. Mechanisms of Development, 94(1–2), 205–208. https://doi.org/10.1016/s0925-4773(00)00315-4

Tamai, K., Semenov, M., Kato, Y., Spokony, R., Liu, C., Katsuyama, Y., Hess, F., Saint-Jeannet, J. P., & He, X. (2000). LDL-receptor-related proteins in Wnt signal transduction. Nature, 407(6803), 530–535. https://doi.org/10.1038/35035117