【2025】
02/14 Stitzer, M.C., Seetharam, A.S., Scheben, A., Hsu, S.-K., Schulz, A.J., AuBuchon-Elder, T.M., El-Walid, M., Ferebee, T.H., Hale, C.O., La, T., Liu, Z.-Y., McMorrow, S.J., Minx, P., Phillips, A.R., Syring, M.L., Wrightsman, T., Zhai, J., Pasquet, R., McAllister, C.A., Malcomber, S.T., Traiperm, P., Layton, D.J., Zhong, J., Costich, D.E., Dawe, R.K., Fengler, K., Harris, C., Irelan, Z., Llaca, V., Parakkal, P., Zastrow-Hayes, G., Woodhouse, M.R., Cannon, E.K., Portwood, J.L., II, Andorf, C.M., Albert, P.S., Birchler, J.A., Siepel, A., Ross-Ibarra, J., Romay, M.C., Kellogg, E.A., Buckler, E.S., Hufford, M.B., 2025. Extensive genome evolution distinguishes maize within a stable tribe of grasses. Evolutionary Biology.
02/07 Adami, A., Garza, R., Gerdes, P., Johansson, P.A., Dorazehi, F., Koutounidou, S., Castilla-Vallmanya, L., Atacho, D.A.M., Sharma, Y., Johansson, J.G., Tam, O., Kirkeby, A., Barker, R.A., Gale-Hammell, M., Douse, C.H., Jakobsson, J., 2025. LINE-1 retrotransposons regulate the exit of human pluripotency and early brain development. Developmental Biology.
01/31 Zeng, R., Shi, Y., Guo, L., Fu, D., Li, M., Zhang, X., Li, Z., Zhuang, J., Yang, X., Zuo, J., Gong, Z., Tian, F., Yang, S., 2025. A natural variant of COOL1 gene enhances cold tolerance for high-latitude adaptation in maize. Cell
【2024】
11/14 Swanson, E.G., Mao, Y., Mallory, B.J., Vollger, M.R., Ranchalis, J., Bohaczuk, S.C., Parmalee, N.L., Bennett, J.T., Stergachis, A.B., 2024. Deaminase-assisted single-molecule and single-cell chromatin fiber sequencing. bioRxiv.
10/31 Li, X., Bie, L., Wang, Y., Hong, Y., Zhou, Z., Fan, Y., Yan, X., Tao, Y., Huang, C., Zhang, Y., Sun, X., Li, J. X. H., Zhang, J., Chang, Z., Xi, Q., Meng, A., Shen, X., Xie, W. & Liu, N. (2024). LINE-1 transcription activates long-range gene expression. Nature Genetics, 56(7), 1494–1502.
09/26 Zhang, X., Marand, A. P., Yan, H. & Schmitz, R. J. (2024). scifi-ATAC-seq: massive-scale single-cell chromatin accessibility sequencing using combinatorial fluidic indexing. Genome Biology, 25(1), 90.
09/19 Gage, J. L., Monier, B., Giri, A. & Buckler, E. S. (2020). Ten Years of the Maize Nested Association Mapping Population: Impact, Limitations, and Future Directions. The Plant Cell, 32(7), 2083–2093.
09/05 Tibbs Cortes, L., Zhang, Z. & Yu, J. (2021). Status and prospects of genome-wide association studies in plants. The Plant Genome, 14(1), e20077.
08/29 Satterlee, J. W., Alonso, D., Gramazio, P., Jenike, K. M., He, J., Arrones, A., Villanueva, G., Plazas, M., Ramakrishnan, S., Benoit, M., Gentile, I., Hendelman, A., Shohat, H., Fitzgerald, B., Robitaille, G. M., Green, Y., Swartwood, K., Passalacqua, M. J., Gagnon, E., … Lippman, Z. B. (2024). Convergent evolution of plant prickles by repeated gene co-option over deep time. Science, 385(6708), eado1663.
08/08 Coale, T. H., Loconte, V., Turk-Kubo, K. A., Vanslembrouck, B., Mak, W. K. E., Cheung, S., Ekman, A., Chen, J.-H., Hagino, K., Takano, Y., Nishimura, T., Adachi, M., Le Gros, M., Larabell, C. & Zehr, J. P. (2024). Nitrogen-fixing organelle in a marine alga. Science, 384(6692), 217–222.
08/01 Bubb, K. L., Hamm, M. O., Min, J. K., Ramirez-Corona, B., Mueth, N. A., Ranchalis, J., Vollger, M. R., Trapnell, C., Cuperus, J. T., Queitsch, C. & Stergachis, A. B. (2024). The regulatory potential of transposable elements in maize. bioRxiv : The Preprint Server for Biology.
04/23 Kakebeen, A. D., Chitsazan, A. D., Williams, M. C., Saunders, L. M. & Wills, A. E. (2020). Chromatin accessibility dynamics and single cell RNA-Seq reveal new regulators of regeneration in neural progenitors. eLife, 9. https://doi.org/10.7554/eLife.52648
04/16 Xu, W., Thieme, M. & Roulin, A. C. (2024). Natural diversity of heat-induced transcription of retrotransposons in Arabidopsis thaliana. In bioRxiv (p. 2024.01.15.575637). https://doi.org/10.1101/2024.01.15.575637
03/26 Klumpe, S., Senti, K. A., Beck, F., Sachweh, J., Hampoelz, B., Ronchi, P., Yeroslaviz, A., Briggs, J. A. G., Brennecke, J., Beck, M. & Plitzko, J. M. (2024). In-cell structure and snapshots of copia retrotransposons in intact tissue by cryo-electron tomography. In bioRxiv (p. 2024.02.21.581285). https://doi.org/10.1101/2024.02.21.581285
03/05 Xia, B., Zhang, W., Zhao, G., Zhang, X., Bai, J., Brosh, R., Wudzinska, A., Huang, E., Ashe, H., Ellis, G., Pour, M., Zhao, Y., Coelho, C., Zhu, Y., Miller, A., Dasen, J. S., Maurano, M. T., Kim, S. Y., Boeke, J. D. & Yanai, I. (2024). On the genetic basis of tail-loss evolution in humans and apes. Nature, 626(8001), 1042–1048.
02/27 Li, Z., Gilbert, C., Peng, H. & Pollet, N. (2024). Systematic annotation of Helitron-like elements in eukaryote genomes using HELIANO. In bioRxiv (p. 2024.02.08.579435). https://doi.org/10.1101/2024.02.08.579435
02/06 Yao, N., Zhang, Z., Yu, L., Hazarika, R., Yu, C., Jang, H., Smith, L. M., Ton, J., Liu, L., Stachowicz, J. J., Reusch, T. B. H., Schmitz, R. J. & Johannes, F. (2023). An evolutionary epigenetic clock in plants. Science, 381(6665), 1440–1445.
【2023】
11/17 Timothy Rabanus-Wallace, M., Wicker, T. & Stein, N. (2023). Replicators, genes, and the C-value enigma: High-quality genome assembly of barley provides direct evidence that self-replicating DNA forms “cooperative” associations with genes in arms races. In bioRxiv (p. 2023.10.01.560391). https://doi.org/10.1101/2023.10.01.560391
11/03 Altemose, N., Maslan, A., Smith, O. K., Sundararajan, K., Brown, R. R., Mishra, R., Detweiler, A. M., Neff, N., Miga, K. H., Straight, A. F. & Streets, A. (2022). DiMeLo-seq: a long-read, single-molecule method for mapping protein-DNA interactions genome wide. Nature Methods, 19(6), 711–723.
10/20 Luo, B., Zhang, Z., Li, B., Zhang, H., Ma, J., Li, J., Han, Z., Zhang, C., Zhang, S., Yu, T., Zhang, G., Ma, P., Lan, Y., Zhang, X., Liu, D., Wu, L., Gao, D., Gao, S., Su, S., … Gao, S. (2023). Chromatin remodeling analysis reveals the RdDM pathway responds to low-phosphorus stress in maize. The Plant Journal: For Cell and Molecular Biology. https://doi.org/10.1111/tpj.16468
09/22, 09/29 Ma, H., Wang, M., Zhang, Y. E. & Tan, S. (2023). The power of “controllers”: Transposon-mediated duplicated genes evolve towards neofunctionalization. Journal of Genetics and Genomics = Yi Chuan Xue Bao, 50(7), 462–472.
09/15 Niu, X., Chen, L., Kato, A. & Ito, H. (2022). Regulatory mechanism of a heat-activated retrotransposon by DDR complex in Arabidopsis thaliana. Frontiers in Plant Science, 13, 1048957.
08/25 Liu, B. & Zhao, M. (2023). How transposable elements are recognized and epigenetically silenced in plants? Current Opinion in Plant Biology, 75, 102428.
08/04, 08/11 Li, C., Gent, J. I., Xu, H., Fu, H., Russell, S. D. & Sundaresan, V. (2022). Resetting of the 24-nt siRNA landscape in rice zygotes. Genome Research, 32(2), 309–323.
07/28 Anderson, S. N., Johnson, C. S., Chesnut, J., Jones, D. S., Khanday, I., Woodhouse, M., Li, C., Conrad, L. J., Russell, S. D. & Sundaresan, V. (2017). The Zygotic Transition Is Initiated in Unicellular Plant Zygotes with Asymmetric Activation of Parental Genomes. Developmental Cell, 43(3), 349–358.e4.
06/30, 07/14 Vernet, A., Meynard, D., Lian, Q., Mieulet, D., Gibert, O., Bissah, M., Rivallan, R., Autran, D., Leblanc, O., Meunier, A. C., Frouin, J., Taillebois, J., Shankle, K., Khanday, I., Mercier, R., Sundaresan, V. & Guiderdoni, E. (2022). High-frequency synthetic apomixis in hybrid rice. Nature Communications, 13(1), 7963.
06/16, 06/30 Khanday, I., Skinner, D., Yang, B., Mercier, R. & Sundaresan, V. (2019). A male-expressed rice embryogenic trigger redirected for asexual propagation through seeds. Nature, 565(7737), 91–95.
06/09 Nelson, J. O., Slicko, A. & Yamashita, Y. M. (2023). The retrotransposon R2 maintains Drosophila ribosomal DNA repeats. Proceedings of the National Academy of Sciences of the United States of America, 120(23), e2221613120.
02/10 Li, S.-F., Zhang, X.-Y., Yang, L.-L., Jia, K.-L., Li, J.-R., Lan, L.-N., Zhang, Y.-L., Li, N., Deng, C.-L. & Gao, W.-J. (2022). Landscape and evolutionary dynamics of Helitron transposons in plant genomes as well as construction of online database HelDB. Journal of Systematics and Evolution. https://doi.org/10.1111/jse.12929
01/27 Review a plant research manuscript in the group.
01/20 Sundaram, V. & Wysocka, J. (2020). Transposable elements as a potent source of diverse cis-regulatory sequences in mammalian genomes. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, 375(1795), 20190347.
