Tzung Fu Hsieh

Lee, J., Lee, S., Park, K., Shin, S.-Y., Frost, J. M., Hsieh, P.-H., … Choi, Y. (2023). Distinct regulatory pathways contribute to dynamic CHH methylation patterns in transposable elements throughout Arabidopsis embryogenesis. FRONTIERS IN PLANT SCIENCE, 14. https://doi.org/10.3389/fpls.2023.1204279

Hsieh, P.-H., Frost, J. M., Choi, Y., Hsieh, T.-F., Zilberman, D., & Fischer, R. L. (2023, April 8). Embryo-specific epigenetic mechanisms reconstitute the CHH methylation landscape during Arabidopsis embryogenesis. https://doi.org/10.1101/2023.04.06.535361

Frost, J. M., Lee, J., Hsieh, P.-H., Lin, S. J. H., Min, Y., Bauer, M., … Choi, Y. (2023). H2A.X promotes endosperm-specific DNA methylation in <i>Arabidopsis thaliana</i>. BMC PLANT BIOLOGY, 23(1). https://doi.org/10.1186/s12870-023-04596-y

Frost, J. M., Lee, J., Hsieh, P.-H., Lin, S. J. H., Min, Y., Bauer, M., … Fischer, R. L. (2023, January 9). H2A.Xmutants exhibit enhanced DNA demethylation inArabidopsis thaliana. https://doi.org/10.1101/2023.01.08.523178

Huang, Y.-C., Wang, Y.-tang, Choong, Y.-ching, Huang, H.-ya, Chen, Y.-ru, Hsieh, T.-F., & Lin, Y.-rong. (2023). How ambient temperature affects the heading date of foxtail millet (Setaria italica). Frontiers in Plant Science, 14. https://doi.org/10.3389/fpls.2023.1147756

Shin, H., Park, J. E., Park, H. R., Choi, W. L., Yu, S. H., Koh, W., … Huh, J. H. (2022, April 28). Admixture of divergent genomes facilitates hybridization across species in the family Brassicaceae. NEW PHYTOLOGIST, Vol. 4. https://doi.org/10.1111/nph.18155

Hsieh, T.-F., Han, Q., Hung, Y.-H., Zhang, C., Bartels, A., Rea, M., … Xiao, W. (2022, October 20). Loss of Linker Histone H1 in the Maternal Genome Influences DEMETER-Mediated Demethylation and Affects the Endosperm DNA Methylation Landscape. https://doi.org/10.1101/2022.10.17.512625

Han, Q., Hung, Y.-H., Zhang, C., Bartels, A., Rea, M., Yang, H., … Hsieh, T.-F. (2022). Loss of linker histone H1 in the maternal genome influences DEMETER-mediated demethylation and affects the endosperm DNA methylation landscape. FRONTIERS IN PLANT SCIENCE, 13. https://doi.org/10.3389/fpls.2022.1070397

Tan, Y., Wang, C., Schneider, T., Li, H., Souza, R. F., Tang, X., … Zhang, D. (2021). Comparative Phylogenomic Analysis Reveals Evolutionary Genomic Changes and Novel Toxin Families in Endophytic Liberibacter Pathogens. MICROBIOLOGY SPECTRUM, 9(2). https://doi.org/10.1128/Spectrum.00509-21

Tan, Y., Wang, C., Schneider, T., Li, H., Souza, R. F., Tang, X., … Zhang, D. (2021, June 5). Comparative phylogenomic analysis reveals evolutionary genomic changes and novel toxin families in endophytic Liberibacter pathogens (Vol. 6). Vol. 6. https://doi.org/10.1101/2021.06.02.446850

Li, M., Cui, Q., Zhang, X.-Q., & Hsieh, T.-F. (2021, September 6). Epigenetic remodeling by DNA glycosylases during rice reproduction. MOLECULAR PLANT, Vol. 14, pp. 1433–1435. https://doi.org/10.1016/j.molp.2021.07.009

Fogarty, M. C., Smith, S. M., Sheridan, J. L., Hu, G., Islamovic, E., Reid, R., … Hsieh, T.-F. (2020). Identification of mixed linkage beta-glucan quantitative trait loci and evaluation of AsCslF6 homoeologs in hexaploid oat. CROP SCIENCE, 60(2), 914–933. https://doi.org/10.1002/csc2.20015

Luan, X., Liu, S., Ke, S., Dai, H., Xie, X.-M., Hsieh, T.-F., & Zhang, X.-Q. (2019). Epigenetic modification of ESP, encoding a putative long noncoding RNA, affects panicle architecture in rice. Rice, 12(1). https://doi.org/10.1186/s12284-019-0282-1

Han, Q., Bartels, A., Cheng, X., Meyer, A., An, Y.-Q. C., Hsieh, T.-F., & Xiao, W. (2019). Epigenetics Regulates Reproductive Development in Plants. Plants, 8(12), 564. https://doi.org/10.3390/plants8120564

Ke, S., Liu, S., Luan, X., Xie, X.-M., Hsieh, T.-F., & Zhang, X.-Q. (2019). Mutation in a putative glycosyltransferase-like gene causes programmed cell death and early leaf senescence in rice. Rice, 12(1). https://doi.org/10.1186/s12284-019-0266-1

Ke, S., Luan, X., Liang, J., Hung, Y.-H., Hsieh, T.-F., & Zhang, X.-Q. (2019). Rice OsPEX1, an extensin-like protein, affects lignin biosynthesis and plant growth. Plant Molecular Biology, 100(1-2), 151–161. https://doi.org/10.1007/s11103-019-00849-3

Zhang, C., Hung, Y.-H., Rim, H. J., Zhang, D., Frost, J. M., Shin, H., … Hsieh, T.-F. (2019). The catalytic core of DEMETER guides active DNA demethylation in Arabidopsis. Proceedings of the National Academy of Sciences, 116(35), 17563–17571. https://doi.org/10.1073/pnas.1907290116

Bartels, A., Han, Q., Nair, P., Stacey, L., Gaynier, H., Mosley, M., … Xiao, W. (2018). Dynamic DNA Methylation in Plant Growth and Development. International Journal of Molecular Sciences, 19(7), 2144. https://doi.org/10.3390/ijms19072144

Lowder, L. G., Zhou, J., Zhang, Y., Malzahn, A., Zhong, Z., Hsieh, T.-F., … Qi, Y. (2018). Robust Transcriptional Activation in Plants Using Multiplexed CRISPR-Act2.0 and mTALE-Act Systems. Molecular Plant, 11(2), 245–256. https://doi.org/10.1016/j.molp.2017.11.010

Hung, Y.-H., Liu, F., Zhang, X.-Q., Xiao, W., & Hsieh, T.-F. (2018). Sexual and Non-sexual Reproduction. In Advances in Botanical Research (Vol. 88, pp. 117–163). https://doi.org/10.1016/bs.abr.2018.09.002

Zeng, X. Y., Tang, R., Guo, H. R., Ke, S. W., Teng, B., Hung, Y. H., … al. (2017). A naturally occurring conditional albino mutant in rice caused by defects in the plastid-localized OsABCI8 transporter. Plant Molecular Biology, 94(1-2), 137–148. https://doi.org/10.1007/s11103-017-0598-4

Lin, J.-Y., & Hsieh, T.-F. (2017). Epigenetic Reprogramming During Plant Reproduction. In Plant Epigenetics (pp. 405–425). https://doi.org/10.1007/978-3-319-55520-1_20

Lin, J.-Y., Le, B. H., Chen, M., Henry, K. F., Hur, J., Hsieh, T.-F., … Goldberg, R. B. (2017). Similarity between soybean and Arabidopsis seed methylomes and loss of non-CG methylation does not affect seed development. Proceedings of the National Academy of Sciences, 114(45), E9730–E9739. https://doi.org/10.1073/pnas.1716758114

Chaffin, A. S., Huang, Y.-F., Smith, S., Bekele, W. A., Babiker, E., Gnanesh, B. N., … Tinker, N. A. (2016). A Consensus Map in Cultivated Hexaploid Oat Reveals Conserved Grass Synteny with Substantial Subgenome Rearrangement. The Plant Genome, 9(2), 0. https://doi.org/10.3835/plantgenome2015.10.0102

Hsieh, T. F. (2016). A Tug of war for DNA methylation. Nature Plants, 2(11).

Mendizabal, I., Shi, L., Keller, T. E., Konopka, G., Preuss, T. M., Hsieh, T.-F., … al. (2016). Comparative Methylome Analyses Identify Epigenetic Regulatory Loci of Human Brain Evolution. Molecular Biology and Evolution, 33(11), 2947–2959. https://doi.org/10.1093/molbev/msw176

Epigenetics: A tug of war for DNA methylation. (2016). Nature Plants. https://doi.org/10.1038/nplants.2016.171

Oliva, M., Butenko, Y., Hsieh, T.-F., Hakim, O., Katz, A., Smorodinsky, N. I., … Ohad, N. (2016). FIE, a nuclear PRC2 protein, forms cytoplasmic complexes inArabidopsis thaliana. Journal of Experimental Botany, 67(21), 6111–6123. https://doi.org/10.1093/jxb/erw373

Lowder, L. G., Zhang, D. W., Baltes, N. J., Paul, J. W., Tang, X., Zheng, X. L., … al. (2015). A CRISPR/Cas9 Toolbox for Multiplexed Plant Genome Editing and Transcriptional Regulation. Plant Physiology, 169(2), 971–985. https://doi.org/10.1104/pp.15.00636

Jeong, C. W., Park, G. T., Yun, H., Hsieh, T.-F., Choi, Y. D., Choi, Y., & Lee, J. S. (2015). Control of Paternally Expressed Imprinted UPWARD CURLY LEAF1, a Gene Encoding an F-Box Protein That Regulates CURLY LEAF Polycomb Protein, in the Arabidopsis Endosperm. PLOS ONE, 10(2), e0117431. https://doi.org/10.1371/journal.pone.0117431

Hsieh, T.-F. (2015). Whole-Genome DNA Methylation Profiling with Nucleotide Resolution. In Methods in Molecular Biology (Vol. 1284, pp. 27–40). https://doi.org/10.1007/978-1-4939-2444-8_2

Mérai, Z., Chumak, N., García-Aguilar, M., Hsieh, T.-F., Nishimura, T., Schoft, V. K., … Tamaru, H. (2014). The AAA-ATPase molecular chaperone Cdc48/p97 disassembles sumoylated centromeres, decondenses heterochromatin, and activates ribosomal RNA genes. Proceedings of the National Academy of Sciences, 111(45), 16166–16171. https://doi.org/10.1073/pnas.1418564111

Ibarra, C. A., Frost, J. M., Shin, J., Hsieh, T.-F., & Fischer, R. L. (2013). Epigenetic Control of Seed Gene Imprinting. In Seed Genomics (pp. 63–82). https://doi.org/10.1002/9781118525524.ch4

Zhang, C., & Hsieh, T.-F. (2013). Heritable Epigenetic Variation and its Potential Applications for Crop Improvement. Plant Breeding and Biotechnology, 1(4), 307–319. https://doi.org/10.9787/pbb.2013.1.4.307

Ibarra, C. A., Feng, X., Schoft, V. K., Hsieh, T.-F., Uzawa, R., Rodrigues, J. A., … Zilberman, D. (2012). Active DNA Demethylation in Plant Companion Cells Reinforces Transposon Methylation in Gametes. Science, 337(6100), 1360–1364. https://doi.org/10.1126/science.1224839

Pedersen, B., Hsieh, T.-F., Ibarra, C., & Fischer, R. L. (2011). MethylCoder: software pipeline for bisulfite-treated sequences. Bioinformatics, 27(17), 2435–2436. https://doi.org/10.1093/bioinformatics/btr394

Hsieh, T.-F., Shin, J., Uzawa, R., Silva, P., Cohen, S., Bauer, M. J., … Fischer, R. L. (2011). Regulation of imprinted gene expression in Arabidopsis endosperm. Proceedings of the National Academy of Sciences, 108(5), 1755–1762. https://doi.org/10.1073/pnas.1019273108

Hsieh, T.-F., Ibarra, C. A., Silva, P., Zemach, A., Eshed-Williams, L., Fischer, R. L., & Zilberman, D. (2009). Genome-Wide Demethylation of Arabidopsis Endosperm. Science, 324(5933), 1451–1454. https://doi.org/10.1126/science.1172417

Stone, S. L., Braybrook, S. A., Paula, S. L., Kwong, L. W., Meuser, J., Pelletier, J., … Harada, J. J. (2008). Arabidopsis LEAFY COTYLEDON2 induces maturation traits and auxin activity: Implications for somatic embryogenesis. Proceedings of the National Academy of Sciences, 105(8), 3151–3156. https://doi.org/10.1073/pnas.0712364105

Huh, J. H., Bauer, M. J., Hsieh, T.-F., & Fischer, R. L. (2008). Cellular Programming of Plant Gene Imprinting. Cell, 132(5), 735–744. https://doi.org/10.1016/j.cell.2008.02.018

Huh, J. H., Bauer, M. J., Hsieh, T.-F., & Fischer, R. (2007). Endosperm gene imprinting and seed development. Current Opinion in Genetics & Development, 17(6), 480–485. https://doi.org/10.1016/j.gde.2007.08.011

Penterman, J., Huh, J. H., Hsieh, T.-F., & Fischer, R. L. (2007). Genomic Imprinting in Arabidopsis thaliana and Zea mays. In Plant Cell Monographs (pp. 219–239). https://doi.org/10.1007/7089_2007_112

Gehring, M., Huh, J. H., Hsieh, T.-F., Penterman, J., Choi, Y., Harada, J. J., … Fischer, R. L. (2006). DEMETER DNA Glycosylase Establishes MEDEA Polycomb Gene Self-Imprinting by Allele-Specific Demethylation. Cell, 124(3), 495–506. https://doi.org/10.1016/j.cell.2005.12.034

Duval, M., & Hsieh, T.-F. (2006). Patenting Applied to Genetic Sequence Information. Biotechnology and Genetic Engineering Reviews, 23(1), 317–330. https://doi.org/10.1080/02648725.2006.10648091

Hsieh, T.-F., & Fischer, R. L. (2005). BIOLOGY OF CHROMATIN DYNAMICS. Annual Review of Plant Biology, 56(1), 327–351. https://doi.org/10.1146/annurev.arplant.56.032604.144118

Hsieh, T.-F., Hakim, O., Ohad, N., & Fischer, R. L. (2003). From flour to flower: how Polycomb group proteins influence multiple aspects of plant development. Trends in Plant Science, 8(9), 439–445. https://doi.org/10.1016/s1360-1385(03)00189-4

Chuang, H.-wen, Hsieh, T.-F., Duval, M., & Thomas, T. L. (2003). Genomic analysis of Arabidopsis gene expression in response to a systemic fungicide. In Genomics of Plants and Fungi (pp. 251–268). CRC Press.

Duval, M., Hsieh, T.-F., Kim, S. Y., & Thomas, T. L. (2002). Molecular characterization of AtNAM: a member of the Arabidopsis NAC domain superfamily. Plant Molecular Biology, 50(2), 237–248. https://doi.org/10.1023/a:1016028530943

Gene expression in the developing mouse retina by EST sequencing and microarray analysis. (2001). Nucleic Acids Research. https://doi.org/10.1093/nar/29.24.4983

Chen, I., Hsieh, T., Thomas, T., & Safe, S. (2001). Identification of estrogen-induced genes downregulated by AhR agonists in MCF-7 breast cancer cells using suppression subtractive hybridization. Gene, 262(1-2), 207–214. https://doi.org/10.1016/s0378-1119(00)00530-8

NUCCIO, M. I. C. H. A. E. L. L., HSIEH, T. Z. U. N. G.-F. U., & THOMAS, T. E. R. R. Y. L. (2000). The use of RT-PCR differential display in single-celled organisms and plant tissues. Differential Display: A Practical Approach, (224), 83.

Characterization and subcellular compartmentation of recombinant 4-hydroxyphenylpyruvate dioxygenase from Arabidopsis in transgenic tobacco. (1999). Plant Physiology. https://doi.org/10.1104/pp.119.4.1507

Garcia, I., Rodgers, M., Pépin, R., Hsieh, T.-F., & Matringe, M. (1998). Plant P-Hydroxyphenylpyruvate Dioxygenase: A Target for New Bleaching Herbicides. In Photosynthesis: Mechanisms and Effects (pp. 3861–3864). https://doi.org/10.1007/978-94-011-3953-3_900

Molecular approaches to identify novel genes expressed in Arabidopsis thaliana. (1997). SAAS Bulletin, Biochemistry and Biotechnology.

Hsieh, T. F., & Thomas, T. L. (1996). Homeobox genes expressed in Arabidopsis embryo. PLANT PHYSIOLOGY, 111(2), 733–733.

Identification of novel mRNAs in immature seeds of Arabidopsis thaliana. (1996). SAAS Bulletin, Biochemistry and Biotechnology.

Chung, Y. W., Hsieh, T.-F., & Wang, C. T. (1991). Identification of phospholipase activities in the exotoxin of Edwardsiella tarda. Reports On Fish Disease Research, 29, 39–46.