Ye, D. *, Walsh, J. T. *, Junker, I. P., & Ding, Y. (2024). Changes in the cellular makeup of motor patterning circuits drive courtship song evolution in Drosophila. bioRxiv, 2024-01. (under revision)

Sawtelle, S., Narayan, L., Ding, Y., Kim, E., Berhman, E. L., Lillvis, J. L., … & Stern, D. L. (2024). Song Torrent: A modular, open-source 96-chamber audio and video recording apparatus with optogenetic activation and inactivation capabilities for Drosophila. bioRxiv, 2024-01.

Li, M., Chen, D. S., Junker, I. P., Szorenyi, F. I., Chen, G. H., Berger, A. J., … & Ding, Y. (2023). Ancestral neural circuits potentiate the origin of a female sexual behavior. bioRxiv, 2023-12. (under review)

Coleman, R. T., Morantte, I., Koreman, G. T., Cheng, M. L., Ding, Y., & Ruta, V. (2023). A modular circuit architecture coordinates the diversification of courtship strategies in Drosophila. bioRxiv, 2023-09. (under revision)

Duckhorn, J. C.*, Junker, I. P.*, Ding, Y.#, and Shirangi, T. R.# (2022). Combined in situ hybridization chain reaction and immunostaining to visualize gene expression in whole-mount Drosophila central nervous systems. In Behavioral Neurogenetics (pp. 1-14). New York, NY: Springer US. (#co-corresponding author)

Arthur, B. J., Ding, Y., Sosale, M., Khalif, F., Kim, E., Waddell, P., … & Stern, D. L. (2021). Songexplorer: a deep learning workflow for discovery and segmentation of animal acoustic communication signals. bioRxiv, 2021-03.

Ding, Y.*, Lillvis, J. L.*, Cande, J., Berman, G. J., Arthur, B. J., Long, X., Min, X, Dickson, B.J., and Stern, D. L. (2019). Neural evolution of context-dependent fly song. Current biology, 29(7), 1089-1099. (*co-first author)

Stern, D. L., Crocker, J., Ding, Y., Frankel, N., Kappes, G., Kim, E., Kuzmickas, R., Lemire, A., Mast, J.D., and Picard, S. (2017). Genetic and transgenic reagents for Drosophila simulans, D. mauritiana, D. yakuba, D. santomea, and D. virilis. G3: Genes, Genomes, Genetics, 7(4), 1339-1347.

Ding, Y., Berrocal, A., Morita, T., Longden, K. D., and Stern, D. L. (2016). Natural courtship song variation caused by an intronic retroelement in an ion channel gene. Nature, 536(7616), 329-332.

Li, X., Fan, D., Zhang, W., Liu, G., Zhang, L., Zhao, L., Fang, X., Chen, L., Dong, Y., Chen, Y. Ding, Y., Zhao, R., Feng, M., Zhu, Y., Feng, Y., Jiang, X., Zhu, D., Xiang, H., Feng, X., Li, S., Wang, J., Zhang, G., Kronforst, M. R., and Wang, W. (2015). Outbred genome sequencing and CRISPR/Cas9 gene editing in butterflies. Nature communications, 6(1), 1-10.

Chen, Y., Frazzitta, A. E., Litvintseva, A. P., Fang, C., Mitchell, T. G., Springer, D. J., Ding, Y., Yuan, G., and Perfect, J. R. (2015). Next generation multilocus sequence typing (NGMLST) and the analytical software program MLSTEZ enable efficient, cost-effective, high-throughput, multilocus sequencing typing. Fungal Genetics and Biology, 75, 64-71.

Xiang, H., Li, X., Dai, F., Xu, X., Tan, A., Chen, L., Zhang, G., Ding, Y., Li, Q., Lian, J., Willden., A., Guo, Q., Xia, Q., Wang, J., and Wang, W. (2013). Comparative methylomics between domesticated and wild silkworms implies possible epigenetic influences on silkworm domestication. BMC genomics, 14(1), 1-11.

Ding, Y., Zhou, Q., and Wang, W. (2012). Origins of new genes and evolution of their novel functions. Annual Review of Ecology, Evolution, and Systematics, 43, 345-363.

Bonasio, R., Li, Q., Lian, J., Mutti, N. S., Jin, L., Zhao, H., Zhang, P., Wen, P., Xiang, H., Ding, Y., Jin, Z., Shen, S., Wang, Z., Wang, W., Wang, J., Berger, S. L., Liebig, J., Zhang, G., and Reinberg, D. (2012). Genome-wide and caste-specific DNA methylomes of the ants Camponotus floridanus and Harpegnathos saltator. Current Biology, 22(19), 1755-1764.

Zhan, Z., Ding, Y., Zhao, R., Zhang, Y., Yu, H., Zhou, Q., Yang, S., Xiang, H., and Wang, W. (2012). Rapid functional divergence of a newly evolved polyubiquitin gene in Drosophila and its role in the trade-off between male fecundity and lifespan. Molecular biology and evolution, 29(5), 1407-1416.

Chen, Y., Ding, Y., Zhang, Z., Wang, W., Chen, J. Y., Ueno, N., and Mao, B. (2011). Evolution of vertebrate central nervous system is accompanied by novel expression changes of duplicate genes. Journal of Genetics and Genomics, 38(12), 577-584.

Ding, Y.*, Zhao, L.*, Yang, S., Jiang, Y., Chen, Y., Zhao, R., Zhang, Y., Zhang, G., Dong, Y., Yu, H., Zhou, Q., and Wang, W. (2010). A young Drosophila duplicate gene plays essential roles in spermatogenesis by regulating several Y-linked male fertility genes. PLoS genetics, 6(12), e1001255. (*co-first author)

Yang, S., Arguello, J. R., Li, X., Ding, Y., Zhou, Q., Chen, Y., Zhang, Y., Zhao, R., Brunet, F., Peng, L., Long, M., and Wang, W. (2008). Repetitive element-mediated recombination as a mechanism for new gene origination in Drosophila. PLoS genetics, 4(1), e3.

Zhou, Q., Zhang, G., Zhang, Y., Xu, S., Zhao, R., Zhan, Z., Li, X., Ding, Y., … & Wang, W. (2008). On the origin of new genes in Drosophila. Genome research, 18(9), 1446-1455.