【2026】
08/21 Kenchanmane Raju, S.K., Zhang, Y., Mahboub, S., Ngu, D.W., Qiu, Y., Harmon, F.G., Schnable, J.C., Roston, R.L., 2024. Rhythmic lipid and gene expression responses to chilling in panicoid grasses. J. Exp. Bot. 75, 5790–5804.
08/07 Kraft, K., Murphy, S.E., Jones, M.G., Shi, Q., Bhargava-Shah, A., Luong, C., Hung, K.L., He, B.J., Li, R., Park, S.K., Montgomery, M.T., Weiser, N.E., Wang, Y., Luebeck, J., Bafna, V., Boeke, J.D., Mischel, P.S., Boettiger, A.N., Chang, H.Y., 2025. Enhancer activation from transposable elements in extrachromosomal DNA. Nat. Cell Biol. 27, 1914–1924.
07/24 Roddy, J.W., Rich, D.H., Wheeler, T.J., 2024. nail: software for high-speed, high-sensitivity protein sequence annotation. bioRxiv.
07/17 Engelhorn, J., Snodgrass, S.J., Kok, A., Seetharam, A.S., Schneider, M., Kiwit, T., Singh, A., Banf, M., Doan, D.T.H., Khaipho-Burch, M., Runcie, D.E., Sánchez-Camargo, V.A., Bader, R., Torres-Rodriguez, J.V., Sun, G., Stam, M., Fiorani, F., Beier, S., Schnable, J.C., Bass, H.W., Hufford, M.B., Stich, B., Frommer, W.B., Ross-Ibarra, J., Hartwig, T., 2025. Genetic variation at transcription factor binding sites largely explains phenotypic heritability in maize. Nat. Genet. 57, 2313–2322.
07/10 Cossu, R.M., Casola, C., Giacomello, S., Vidalis, A., Scofield, D.G., Zuccolo, A., 2017. LTR retrotransposons show low levels of unequal recombination and high rates of intraelement gene conversion in large plant genomes. Genome Biol. Evol. 9, 3449–3462.
06/26 Hasan, M.M., Yin, L., Wang, M., Pawlowski, W.P., Zhao, M., 2025. mop1 affects maize recombination landscapes by modulating methylation of MITEs near genes in open chromatin. Nat. Commun. 16, 10476.
06/12 Lin, A.T., Fairbanks, R.A., Barba-Montoya, J., Liu, H.-L., Kistler, L., 2025. A legacy of genetic entanglement with wolves shapes modern dogs. Proc. Natl. Acad. Sci. U.S.A. 122, e2421768122.
06/05 Dai, D., Chen, K., Tao, J., Williams, B.P., 2026. Aging drives a program of DNA methylation decay in plant organs. Science 391, 6784.
05/22 Li, B., Li, T., Wang, D., Yang, Y., Tan, P., Wang, Y., Yang, Y.-G., Jia, S., Au, K.F., 2025. Zygotic activation of transposable elements during zebrafish early embryogenesis. Nat. Commun. 16, 3692.
04/03 Li, Z., Gilbert, C., Peng, H., Pollet, N., 2024. Discovery of numerous novel Helitron-like elements in eukaryote genomes using HELIANO. Nucleic Acids Res. 52, e79.
03/27 Ding, C., Chen, G., Luan, S., Gao, R., Fan, Y., Zhang, Y., Wang, X., Li, G., Foda, M.F., Yan, J., Li, X., 2025. Simultaneous profiling of chromatin-associated RNA at targeted DNA loci and RNA-RNA interactions through TaDRIM-seq. Nat. Commun. 16, 1500.
03/13 Krause, G.R., Shands, W., Wheeler, T.J., 2024. Sensitive and error-tolerant annotation of protein-coding DNA with BATH. Bioinform. Adv. 4, vbae088.
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02/06 Zhou, S., Li, X., Liu, Q., Zhao, Y., Jiang, W., Wu, A., Zhou, D.-X., 2021. DNA demethylases remodel DNA methylation in rice gametes and zygote and are required for reproduction. Mol. Plant 14, 1569–1583.
01/30 Li, X., Zhu, B., Lu, Y., Zhao, F., Liu, Q., Wang, J., Ye, M., Chen, S., Nie, J., Xiong, L., Zhao, Y., Wu, C., Zhou, D.-X., 2024. DNA methylation remodeling and the functional implication during male gametogenesis in rice. Genome Biol. 25, 84.
01/23 Qi, Y., Chen, Y., Wu, Y., Guo, Y., Gao, M., Zhang, F., Liao, X., Shang, X., 2025. CREATE: a novel attention-based framework for efficient classification of transposable elements. Brief. Bioinform. 26.
【2025】
12/11 Yang, F., Su, W., Chung, O.W., Tracy, L., Wang, L., Ramsden, D.A., Zhang, Z.Z.Z., 2023. Retrotransposons hijack alt-EJ for DNA replication and eccDNA biogenesis. Nature 620, 218–225.
12/04 Staut, J., Pérez, N.M., Ferrando, A.M., Dissanayake, I., Vandepoele, K., 2025. A map of integrated cis-regulatory elements enhances gene-regulatory analysis in maize. Plant Commun. 6, 101376.
11/20 Nguyen, V.H., Mittelsten Scheid, O., Gutzat, R., 2025. Heat stress response and transposon control in plant shoot stem cells. Plant Physiol. 197, kiaf110.
11/13 Tossolini, I., Mencia, R., Arce, A.L., Manavella, P.A., 2025. The genome awakens: transposon-mediated gene regulation. Trends Plant Sci. 30, 857–871.
10/30 Jin, W., Yu, C., Zhang, Y., Cao, C., Xia, T., Song, G., Cai, Z., Xue, Y., Zhu, B., Xu, R.-M., 2025. Mechanism of DNA targeting by human LINE-1. Science 390, eadu3433.
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06/27 Lynch, R.C., Padgitt-Cobb, L.K., Garfinkel, A.R., Knaus, B.J., Hartwick, N.T., Allsing, N., Aylward, A., Bentz, P.C., Carey, S.B., Mamerto, A., Kitony, J.K., Colt, K., Murray, E.R., Duong, T., Chen, H.I., Trippe, A., Harkess, A., Crawford, S., Vining, K., Michael, T.P., 2025. Domesticated cannabinoid synthases amid a wild mosaic cannabis pangenome. Nature 643, 1001–1010.
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06/13 Song, X., Tang, S., Liu, H., Meng, Y., Luo, H., Wang, B., Hou, X.-L., Yan, B., Yang, C., Guo, Z., Wang, L., Jiang, S., Deng, X., Cao, X., 2025. Inheritance of acquired adaptive cold tolerance in rice through DNA methylation. Cell.
06/06 Guo, D., Li, Y., Lu, H., Zhao, Y., Kurata, N., Wei, X., Wang, A., Wang, Y., Zhan, Q., Fan, D., Zhou, C., Lu, Y., Tian, Q., Weng, Q., Feng, Q., Huang, T., Zhang, L., Gu, Z., Wang, C., Wang, Z., Wang, Z., Huang, X., Zhao, Q., Han, B., 2025. A pangenome reference of wild and cultivated rice. Nature 1–10.
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【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.
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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.
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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.
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【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
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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
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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.