• Original Papers
• Reviews
• Book Chapters and Others
• Books

Original Papers

2024

• Peng, Z., Bao, L., Shi, B., and Shi, Y.-B. (2024) Protein arginine methyltransferase 1 is required for the maintenance of adult small intestinal and colonic epithelial cell homeostasis. Int. J. Biol. Sci. 20(2): 554-568. doi: 10.7150/ijbs.89958
• Fu, L., Wang, S., Liu, L., Shibata, Y., Okada, M., Luu, N., and Shi, Y.-B. (2024) Simplifying genotyping of mutants from genome editing with parallel qPCR-based iGenotype index. Cells. 13: 247, 1-14. https://doi.org/10.3390/cells13030247
• Bao, L., Fu, L., Su, Y., Chen, Z., Peng, Z., Sun, L., Gonzalez, F.J., Wu, C., Zhang, H., Shi, B., and Shi, Y.-B. (2024) Amino acid transporter SLC7A5 regulates Paneth cell function to affect the intestinal inflammatory response. Int. J. Biol. Sci. In press.

2023

• Tanizaki, Y., Zhang, H., Shibata, Y., and Shi, Y.-B. (2023) Organ-specific effects on target binding due to knocking out thyroid hormone receptor α during Xenopus metamorphosis. Development, Growth & Differentiation 65(1):23-28. doi: 10.1111/dgd.12825 (Cover photo).
• Wang, S., Shibata, Y., Tanizaki, Y., Zhang, H., Yan, W., Fu, L., and Shi, Y.-B. (2023) Comparative analysis of transcriptome profiles reveals distinct and organ-dependent genomic and nongenomic actions of thyroid hormone in Xenopus tropicalis tadpoles. Thyroid 33(4):511-522. doi: 10.1089/thy.2022.0469
• Tanizaki, Y., Wang, S., Zhang, H., Shibata, Y., and Shi, Y.-B. (2023) Canonical Wnt signaling is activated during thyroid hormone-dependent liver metamorphosis in Xenopus tropicalis. iScience 26:106301, 1-19. https://doi.org/10.1016/j.isci.2023.106301
• Wang, S., Shibata, Y., Fu, L., Tanizaki, Y., Luu, N., Bao, L., Peng, Z., and Shi, Y.-B. (2023) Thyroid hormone receptor knockout prevents the loss of Xenopus tail regeneration capacity at metamorphic climax. Cell & Bioscience. 13:40, 1-14. doi.org/10.1186/s13578-023-00989-6
• Park, G., Fukasawa, K., Horie, T., Masuo, T., Inaba, T., Tatsuno, T., Yamada, T., Tokumura, K., Iwahashi, S., Iezaki, T., Kaneda, K., Kato, Y., Ishigaki, Y., Mieda, M., Tanaka, T., Ogawa, K., Ochi, H., Sato, S., Shi, Y.-B., Inoue, H., Lee, H., Hinoi, E. (2023) l-type amino acid transporter 1 in hypothalamic neurons in mice maintains energy and bone homeostasis. JCI Insight. 8(7):e154925, 1-19. https://doi.org/10.1172/jci.insight.154925
• Fu, L., Ma, E., Okada, M., Shibata, Y., and Shi, Y.-B. (2023) Competitive PCR with dual fluorescent primers enhances the specificity and reproducibility of genotyping animals generated from genome editing. Cell & Bioscience 13:83, 1-5. https://doi.org/10.1186/s13578-023-01042-2

2022

• Fu, L., Crawford, L., Tong, A., Luu, N., Tanizaki, Y., and Shi, Y.-B. (2022) Sperm associated antigen 7 (SPAG7) is activated by T3 during Xenopus tropicalis metamorphosis via a thyroid hormone response element (TRE) within the first intron. Development, Growth & Differentiation 64:48–58.
• Tanizaki, Y., Shibata, Y., Zhang, H., and Shi, Y.-B. (2022) Thyroid hormone receptor α controls the hindlimb metamorphosis by regulating cell proliferation and Wnt signaling pathways in Xenopus tropicalis. International Journal of Molecular Sciences 23:1223, 1-18. https://doi.org/10.3390/ijms23031223
• Tanizaki, Y., Zhang, H., Shibata, Y., and Shi, Y.-B. (2022) Thyroid hormone receptor α controls larval intestinal epithelial cell death by regulating the CDK1 pathway. Communications Biology  5:112, 1-10. https://doi.org/10.1038/s42003-022-03061-0
• Liu, Y., Wang, J., Chen, J., Wu, S., Zeng, X., Xiong, Q., Guo, Y., Sun, J., Song, F., Xu, J., Yuan, S., Li, C., He, Y., Wang, M., Chen, L., Shi, Y.-B., M. Guo, Guo, D., and Sun, G. (2022) Upregulation of miR-520c-3p via hepatitis B virus drives hepatocellular migration and invasion by the PTEN/AKT/NF-κB axis. Mol Ther Nucleic Acids 29:47-63. https://doi.org/10.1016/j.omtn.2022.05.031
• Fu, L., Liu, R., Ma, V., and Shi, Y.-B. (2022) Upregulation of Protooncogene Ski by Thyroid Hormone in the Intestine and Tail during Xenopus Metamorphosis. General and Comparative Endocrinology 328:114102, 1-8. doi.org/10.1016/j.ygcen.2022.114102

2021

• Tanizaki, Y., Shibata, Y.,  Zhang, H., and Shi, Y.-B. (2021) Analysis of thyroid hormone receptor α knockout tadpoles reveals that the activation of cell cycle program is involved in thyroid hormone-induced larval epithelial cell death and adult intestinal stem cell development during Xenopus tropicalis metamorphosis. Thyroid  31:128-142. https://doi.org/10.1089/thy.2020.0022
• Shibata, Y., Tanizaki, Y., Zhang, H., Lee, H., Dasso, M., and Shi, Y.-B. (2021) Thyroid hormone receptor is essential for larval epithelial apoptosis and adult epithelial stem cell development but not adult intestinal morphogenesis during Xenopus tropicalis metamorphosis. Cells 10:536, 1-20. https://doi.org/10.3390/cells10030536
• Tanizaki, Y., Bao, L., Shi, B., and Shi, Y.-B. (2021) A role of endogenous histone acetyltransferase steroid hormone receptor coactivator (SRC) 3 in thyroid hormone signaling during Xenopus intestinalmetamorphosis. Thyroid  31:692-702. DOI: 10.1089/thy.2020.0410 (Cover photo)
• Wang, S. and Shi, Y.-B. (2021) Evolutionary divergence in tail regeneration between Xenopus laevis and Xenopus tropicalis. Cell & Bioscience 11:71, 1-4. https://doi.org/10.1186/s13578-021-00582-9
• Wang, H.-X., Qin, X.-H., Shen, J., Liu, Q.-H., Shi, Y.-B., and Xue, L. (2021) Proteomic analysis reveals that placenta-specific protein 9 inhibits proliferation and stimulates motility of human bronchial epithelial cells. Frontiers in Oncology-Molecular and Cellular Oncology 11:628480. doi: 10.3389/fonc.2021.628480
• Xue, L., Bao, L., Roediger, J., Su, Y., Shi, B., and Shi, Y.-B. (2021) Protein arginine methyltransferase 1 regulates cell proliferation and differentiation in adult mouse adult intestine. Cell & Bioscience 11: 113, 1-17. https://doi.org/10.1186/s13578-021-00627-z
• Trofka, A., Huang, B.-L., Zhu, J., Heinz, W.F., Magidson, V., Shibata, Y., Shi, Y.-B., Tarchini, B., Stadler, H.S., Kabangu, M., Al Haj Baddar, N.W., Voss, S.R., and Mackem, S. (2021) Genetic basis for an evolutionary shift from ancestral preaxial to postaxial limb polarity in non-urodele vertebrates. Current Biol. 31: 4923–4934.
• Wang, S., Liu, L., Shi, Y.-B. *, Jiang, J.* (2021) Transcriptome profiling reveals gene regulation programs underlying tail development in the Ornamented Pygmy frog Microhyla fissipes. Frontiers In Bioscience-Landmark 26(11):1001-1012, DOI:10.52586/5004 (*Corresponding Authors)
• Wu, Y., Han, X., Su, Y., Glidewell, M., Daniels, J.S., Liu, J., Sengupta, T., Rey-Suarez, I., Fischer, R., Patel, A., Combs, C., Sun, J., Wu, X., Christensen, R., Smith, C., Bao, L., Sun, Y., Duncan, L.H., Chen, J., Pommier, Y., Shi, Y.-B., Murphy, E., Roy, S., Upadhyaya, A., Colón-Ramos, D., La Riviere, P., Shroff, H. (2021) Multiview super-resolution microscopy. Nature 600: 279-284. https://doi.org/10.1038/s41586-021-04110-0

2020

• Fu, L., Li, C., Na, W., and Shi, Y.-B. (2020) Thyroid hormone activates Xenopus MBD3 gene via an intronic TRE in vivo. Frontiers In Bioscience-Landmark 25:437-451.
• Poncet, N., Gierliński, M., Melanie Febrer, M., Lipina, C., Halley, P. A., Shi, Y.-B., Yamaguchi, T. P., Taylor, P. M., Storey, K. G. (2020) Wnt regulates amino acid transporter Slc7a5 and so constrains the integrated stress response in mouse embryos. EMBO Reports 21: e48469, 1-20
• Shibata, Y., Wen, L., Okada, M., and Shi, Y.-B. (2020) Organ-specific requirements for thyroid hormone receptor ensure temporal coordination of tissue-specific transformations and completion of Xenopus metamorphosis. Thyroid 30: 300–313. https://doi.org/10.1089/thy.2019.0366
• Nakajima, K., Tanizaki, Y., Luu, N., Zhang, H., and Shi, Y.-B. (2020) Comprehensive RNA-seq analysis of notochord-specific genes induced during Xenopus tropicalis tail resorption. General and Comparative Endocrinology 287:113349, 1-9. doi.org/10.1016/j.ygcen.2019.113349
• Shibata, Y., Okada, M., Miller, T.C., and Shi, Y.-B. (2020) Knocking out histone methyltransferase PRMT1 leads to stalled tadpole development and lethality in Xenopus tropicalis. BBA General Subjects 1864(3):129482, 1-8; doi: 10.1016/j.bbagen.2019.129482
• Na, W., Fu, L., Luu, N., and Shi, Y.-B. (2020) Thyroid hormone directly activates mitochondrial fission process 1 (Mtfp1) gene transcription during adult intestinal stem cell development and proliferation in Xenopus tropicalis. General and Comparative Endocrinology 299:113590, 1-8. https://doi.org/10.1016/j.ygcen.2020.113590
• Shibata, Y.,  Tanizaki, Y., and Shi, Y.-B. (2020) Thyroid hormone receptor beta is critical for intestinal remodeling during Xenopus tropicalis metamorphosis. Cell & Bioscience 10:46, 1-15. doi: 10.1186/s13578-020-00411-5 (recipient of the Ming K. Jeang Award for Excellence in Cell & Bioscience for 2020)
• Na, W., Fu, Li., Luu, N., and Shi, Y.-B. (2020) Direct activation of tRNA methyltransferase-like 1 (Mettl1) gene by thyroid hormone receptor implicates a role in adult intestinal stem cell development and proliferation during Xenopus tropicalis metamorphosis. Cell & Bioscience 10:60, 1-10 https://doi.org/10.1186/s13578-020-00423-1

2019

• Wang, J., Chen, J., Wei, M., Wu, S., Zeng, X., Xiong, Q., Song, F., Xiao, Y., Bao, Y., Liu, Z., Li, C., Guo, M., Shi, Y.-B., Sun, G., and Guo, D. (2019) HBV inducing autophagy to increase its replication by the axis of miR-192-3p-XIAP via NFkB signal. Hepatology 69:974-992.
• Bao, L., Roediger, J., Park, S., Fu, L., Shi, B., Cheng, S.-Y., and Shi, Y.-B (2019) Thyroid Hormone Receptor Alpha Mutations Lead to Epithelial Defects in the Adult Intestine in a Mouse Model of Resistance to Thyroid Hormone. Thyroid 29(3):439-448.
• Wang, S., Liu, L., Liu, J., Zhu, W., Tanizaki, Y., Fu, L., Bao, L., Shi, Y.-B., Jiang, J. (2019) Gene expression program underlying tail resorption during thyroid hormone-dependent metamorphosis of the ornamented pygmy frog Microhyla fissipes. Frontiers in Endocrinology 10:11, 1-12; doi: 10.3389/fendo.2019.00011  
• Nakajima, K., Tazawa, I., and Shi, Y.-B. (2019) A unique role of thyroid hormone receptor b in regulating notochord resorption during Xenopus metamorphosis. General and Comparative Endocrinology, 277: 66–72.
• Ozaki, K., Yamada, T., Horie, T., Ishizaki, A., Hiraiwa, M., Iezaki, T., Park, G., Kazuya Fukasawa, K., Kamada, H., Kaneda, K., Ogawa, K., Ochi, H., Sato, S., Kobayashi, Y., Shi, Y.-B., Taylor, P.M., Hinoi, E. (2019) System L amino acid transporter LAT1 regulates osteoclastogenesis and bone homeostasis via the mTORC1 pathway. Science Signaling 12:eaaw3921, 1-14

2018

• Okada, M. and Shi, Y.-B. (2018). EVI and MDS/EVI are required for adult intestinal stem cell formation during postembryonic vertebrate development. FASEB J 32:431–439.

2017

• Wen, L., Shibata, Y., Su, D., Fu, L., Luu, N., and Shi, Y.-B. (2017) Thyroid hormone receptor α controls developmental timing and regulates the rate and coordination of tissue specific metamorphosis in Xenopus tropicalis.Endocrinology 158(6):1985-1998.
• Okada, M., Miller, T.C., Wen, L., and Shi, Y.-B. (2017). A balance of Mad and Myc expression dictates larval cell apoptosis and adult stem cell development during Xenopus intestinal metamorphosis. Cell Death & Disease 8(5):e2787, 1-10; doi:10.1038/cddis.2017.
• Wen, L., Fu, L., and Shi, Y.-B. (2017) Histone methyltransferase Dot1L is a coactivator for thyroid hormone receptor during Xenopus development. FASEB J 31: 4821-4831
• Okada, M., Miller, T.C., Roediger, J., Shi, Y.-B. and Schech, J. M. (2017). An efficient, simple, and non-invasive procedure for genotyping vertebrate laboratory animals. Journal of the American Association for Laboratory Animal Science (JAALAS) 56:1–4.
• Fu, L., Das, D., Matsuura, K., Fujimoto, K., Heimeier, R.A., and Shi, Y.-B. (2017) Genome-wide identification of thyroid hormone receptor targets in the remodeling intestine during Xenopus tropicalis metamorphosis. Scientific Reports 7:6414, 1-11; doi:10.1038/s41598-017-06679-x.
• Luu, N., Fu, L., Fujimoto, K., and Shi, Y.-B. (2017) Direct regulation of histidine ammonia-lyase 2 gene by thyroid hormone in the developing adult intestinal stem cells. Endocrinology 158(4):1022-1033.

2016

• Hasebe, T., Fujimoto, K., Kajita, M., Fu, L., Shi, Y.-B., and Ishizuya-Oka, A. (2016) Thyroid hormone-induced activation of Notch signaling is required for adult intestinal stem cell development during Xenopus laevis metamorphosis. Stem Cells 35:1028–1039.
• Fu, L., Wen, L., Luu, N., and Shi, Y.-B. (2016) A simple and efficient method to visualize and quantify the efficiency of chromosomal mutations from genome editing. Scientific Reports 6:35488, 1-10. Highlighted in Xenbase Nov. 2016 (http://www.xenbase.org/entry/).

2015

• Okada, M., Wen, L., Miller, T.C., Su, D., and Shi, Y.-B. (2015) Molecular and cytological analyses reveal distinct transformations of intestinal epithelial cells during Xenopus metamorphosis. Cell & Bioscience 5:74, 1-12.
• Xiong, L.-H., Cui, R., Zhang, Z.-L., Tu, J.-W., Shi, Y.-B., and Pang, D.-W.(2015) Harnessing Intracellular Biochemical Pathways for In Vitro Synthesis of Designer Tellurium Nanorods. Small 11(40): 5416–5422.
• Wen, L., Fu, L., Guo, X., Chen, Y., and Shi, Y.-B. (2015) Histone methyltransferase Dot1L plays a role in postembryonic development in Xenopus tropicalis. FASEB J. 29, 385-393
• Wen, L., and Shi, Y.-B. (2015) Unliganded thyroid hormone receptor α controls developmental timing in Xenopus tropicalis. Endocrinology 156(2):721–734. Featured in Endocrine News (Jan. 2015:12)’; Cell & Bioscience 2015, 5; and Endocrinology 2015, 156(2):409–410.
• Wen, L., Hasebe, T., Miller, T.C., Ishizuya-Oka, A., and Shi, Y.-B. (2015) A requirement for hedgehog signaling in thyroid hormone-induced postembryonic intestinal remodeling. Cell & Bioscience 5:13, 1-12. 
• Wang, F., Shi, Z., Cui, Y., Guo, X., Shi, Y.-B., and Chen, Y. (2015) Targeted gene disruption in Xenopus laevis using CRISPR/Cas9. Cell & Bioscience 5:15, 1-5.
• Okada, M., Miller, T.C., Fu, L., and Shi, Y.-B. (2015) Direct activation of amidohydrolase domain-containing 1 gene by thyroid hormone implicates a role in the formation of adult intestinal stem cells during Xenopus metamorphosis.Endocrinology 156: 3381–3393. Highlighted in Intestinal Cell News 2015, 1.13..

2014

• Poncet, N., Mitchell, F.E., Ibrahim, A.F.M., McGuire, V.A., English, G., Arthur, S.C., and Shi, Y.-B*., and Taylor, P.M*. (2014) The catalytic subunit of the System L1 amino acid transporter (Slc7a5) facilitates nutrient signaling in mouse skeletal muscle. PLoS One 9(2): e89547,1-14 (*Corresponding Authors)
• Xiong, L.-H., Cui, R., Zhang, Z.-L., Yu, X., Xie, Z.-X., Shi, Y.-B., and Pang, D.-W.(2014) Uniform Fluorescent Nanobioprobes for Pathogen Detection. ACS Nano 8 (5), 5116–5124. Highlighted in Cell & Bioscience 2014, 4:34
• Liu, S.-L., Zhang, L.-J., Zhang, Z.-L., Wang, Z.-G., Wu, Q.-M., Sun, E.-Z., Shi, Y.-B., and Pang, D.-W.(2014) Globally Visualizing the Microtubule-Dependent Infection Behaviors of Influenza Virus in Live Cells. Analytical Chemistry 86 (8), 3902–3908
• Sun, G., Fu, L., Wen, L., and Shi, Y.-B. (2014) Activation of Sox3 gene by thyroid hormone in the developing adult intestinal stem cell during Xenopus metamorphosis. Endocrinology 155(12):5024–5032

2013

• Miller, T.C., Sun, G., Hasebe, T., Fu, L., Heimeier, R.A., Das, B., Ishizuya-Oka, A., and Shi, Y.-B. (2013) Tissue-specific upregulation of MDS/EVI gene transcripts in the intestine by thyroid hormone during Xenopus metamorphosis. PLoS One 8:e55585, 1-7.
• Sinclair, L. V., Rolf, J., Emslie, E., Shi, Y.-B., Taylor, P. M., and Cantrell, D. A. (2013) Antigen receptor control of amino acid transport coordinates the metabolic re-programming that is essential for T cell differentiation. Nature Immunology14, 500-8. (Editor’s choice, Science, 2013. VOL 340, 10).
• Xue, L., Cai, J.-Y., Ma, J., Huang, Z., Guo, M.-X., Fu, L., Shi, Y.-B.*, and Li, W.-X*. (2013) Global expression profiling reveals genetic programs underlying the developmental divergence between mouse and human embryogenesis. BMC Genomics. 14, 568 (*Corresponding Authors)
• Sun, G., Heimeier, R.A., Fu, L., Hasebe, T., Das, B., Ishizuya-Oka, A., and Shi, Y.-B. (2013) Expression profiling of intestinal tissues implicates novel genes and pathways essential for adult stem cell development. Endocrinology 154(11), 4396–4407  
• Luu, N., Wen, L., Fu, L., Fujimoto, K., and Shi, Y.-B.*, and Sun, G*. (2013) Differential regulation of two histidine ammonia-lyase genes during Xenopus development implicates distinct functions during thyroid hormone-induced formation of adult stem cells. Cell & Bioscience 3:43, 1-11 (*Corresponding Authors).

2012

• Matsuura, K., Fujimoto, K., Fu, L., and Shi, Y.-B. (2012) Liganded thyroid hormone receptor induces nucleosome removal and histone modifications to activate transcription during larval intestinal cell death and adult stem cell development. Endocrinology 153, 961-972.
• Helbing, C.C., Wagner, M.J., Pettem, K., Johnston, J., Heimeier, R.A., Veldhoen, N., Jirik, F.R., Shi, Y.-B., and Browder, L.W. (2012) Modulation of thyroid hormone-dependent gene expression in Xenopus laevis by INhibitor of Growth (ING) proteins. PLoS One. 6: e28658, 1-11.
• Hasebe, T., Kajita, M., Fu, L., Shi, Y.-B., and Ishizuya-Oka, A. (2012) Thyroid hormone-induced Sonic hedgehog signal up-regulates its own pathway in a paracrine manner in the Xenopus laevis intestine during metamorphosis. Dev Dyn. 241, 403-414.
• Fujimoto, K., Matsuura, K., Hu-Wang, E., Lu, R., and Shi, Y.-B. (2012) Thyroid hormone activates protein arginine methyltransferase 1 expression by directly inducing c-Myc transcription during Xenopus intestinal stem cell development. J. Biol. Chem. 287, 10039-10050.
• Fu, L., Sun, G., Fiorentino, M., and Shi, Y.-B. (2012) Characterization of Xenopus Tissue Inhibitor of Metalloproteinases-2: A role in regulating matrix metalloproteinase activity during development. PLoS One, 7: e36707, 1-8.
• Fujimoto, K., Matsuura, K., Das, B., Fu, L., and Shi, Y.-B. (2012) Direct activation of Xenopus iodotyrosine deiodinase by thyroid hormone receptor in the remodeling intestine during amphibian metamorphosis. Endocrinology 153(10), 5082-9.
• Sterling, J., Fu, L., Matsuura, K., and Shi, Y.-B. (2012) Cytological and morphological analyses reveal distinct features of intestinal development during Xenopus tropicalis metamorphosis . PLoS One 7:e47407, 1-10.
• Matsuura, K., Fujimoto, K., Das, B., Fu, L., Lu, C.D., and Shi, Y.-B. (2012) Histone H3K79 methyltransferase Dot1L is directly activated by thyroid hormone receptor during Xenopus metamorphosis. Cell & Bioscience 2:25, 1-10.

2011

• Hasebe, T., Buchholz, D.R., Shi, Y.-B., and Ishizuya-Oka, A. (2011) Epithelial-connective tissue interactions induced by thyroid hormone receptor are essential for adult stem cell development in the Xenopus laevis intestine. Stem Cells 29 (1), 154-61.
• Sato, Y., Heimeier, R.A., Li, C., Deng, C., and Shi, Y.-B. (2011) Extracellular domain of CD98hc is required for early murine development. Cell & Bioscience 1:7, 1-12.
• Song, E.-Q., Hu, J., Wen, C.-Y., Tian, Z.-Q., Yu, X., Zhang, Z.-L., Shi, Y.-B., and Pang, D.-W. (2011) Fluorescent-Magnetic-Biotargeting Multifunctional Nanobioprobes for Detecting and Isolating Multiple Types of Tumor Cells. ACS Nano. 5(2), 761-70.

2010

• Heimeier, R.A., Das, B., Buchholz, D.R., Fiorentino. M., and Shi, Y.-B. (2010) Studies on Xenopus laevis intestine reveal biological pathways underlying vertebrate gut adaptation from embryo to adult. Genome Biology, 11:R55, 1-20.
• Yi, H., Xue, L., Guo, M.-X., Ma, J., Zeng, Y., Wang, W., Cai, J.-Y., Hu, H.-M., Shu, H.-B., Shi, Y.-B., and Li, W.-X. (2010) Gene Expression Atlas for Human Embryogenesis. FASEB J. 24, 3341-3350 (*Corresponding Authors)
• Sun, G., Hasebe, T., Fujimoto, K., Lu, R., Fu, L., Matsuda, H., Kajita, M., Ishizuya-Oka, A., and Shi, Y.-B. (2010) Spatio-temporal expression profile of stem cell-associated gene LGR5 in the intestine during thyroid hormone-dependent metamorphosis in Xenopus laevis. PLoS One, 5: e13605, 1-9.
• Matsuda, H., and Shi, Y.-B. (2010) An essential and evolutionarily conserved role of protein arginine methyltransferase 1 for adult intestinal stem cells during postembryonic development. Stem Cells 28, 2073-2083.

2009

• Fu, L., Das, B., Mathew, S., and Shi, Y.-B. (2009) Genome-wide identification of Xenopus matrix metalloproteinases: conservation and unique duplications in amphibians. BMC Genomics. 10, 81 (1-18).
• Das, B., Heimeier, R.A., Buchholz, D.R., and Shi, Y.-B. (2009) Identification of direct thyroid hormone response genes reveals the earliest gene regulation programs during frog metamorphosis. J. Biol. Chem. 284, 34167-34178.
• Wang, Y., Mukhopadhyay, D., Mathew, S., Hasebe, T., Heimeier, R., Azuma, Y., Kolli, N., Shi, Y.-B., Wilkinson, K.D., and Dasso, M. (2009) Identification and Developmental Expression of Xenopus laevis SUMO Proteases. PLoS One 4: e8462, 1-10.
• Fiorentino, M., Fu, L., and Shi, Y.-B. (2009) Mutational analysis of the cleavage of the cancer-associated laminin receptor by stromelysin-3 reveals the contribution of flanking sequences to site recognition and cleavage efficiency. International Journal of Molecular Medicine. 23, 389-397.
• Mathew, S., Fu, L., Fiorentino, M., Matsuda, H., Das, B., and Shi, Y.-B. (2009) Differential regulation of cell type specific apoptosis by stromelysin-3: A potential mechanism via the cleavage of the laminin receptor during tail resorption in Xenopus laevis. J. Biol. Chem. 284(27), 18545-56.
• Ishizuya-Oka, A., Hasebe, T., Buchholz, D. R., Kajita, M., Fu, L., and Shi, Y.-B. (2009) The Origin of the adult intestinal stem cells induced by thyroid hormone in Xenopus laevis. The FASEB J. 23(8), 2568-75.
• Song, E.-Q., Zhang, Z.-L., Luo, Q.-Y., Wen, L., Shi, Y.-B., and Pang, D.-W. (2009) Tumor Cell Targeting Using Folate-Conjugated Fluorescent Quantum Dots And Receptor-Mediated Endocytosis. Clinical Chemistry. 55(5), 955-63.
• Heimeier, R.A., Das, B., Buchholz, D.R., and Shi, Y.-B. (2009) The xenoestrogen bisphenol A inhibits postembryonic vertebrate development by antagonizing gene regulation by thyroid hormone. Endocrinology 150(6), 2964-73. Featured in Endocrine News (May, 2009).
• Wang, D., Xia, X., Lu, Y., Oetting, A., Walker, R.L., Zhu, Y., Meltzer, P., Cole, P.A., Shi, Y.-B., P. Yen (2009) Negative Regulation of TSHα Target Gene by Thyroid Hormone Involves Histone Acetylation and Corepressor Complex Dissociation. Mol. Endocrinol. 23(5), 600-9.
• Sato, Y., Ding, A., Heimeier, R. A., Yousef, A. F., Mymryk, J. S., Walfish, P. G., and Shi, Y.-B. (2009) The adenoviral E1A protein displaces corepressors and relieves gene repression by unliganded thyroid hormone receptors in vivo. Cell Res. 19, 783-792..
• Matsuda, H., Paul, B. D., Choi, C. Y., Hasebe, T., and Shi, Y.-B. (2009) Novel functions of protein arginine methyltransferase 1 in thyroid hormone receptor-mediated transcription and in the regulation of metamorphic rate in Xenopus laevis. Mol. Cell. Biol. 29, 745-757.

2008

• Wang, X., Matsuda, H., and Shi, Y.- B. (2008) Developmental regulation and function of thyroid hormone receptors and 9-cis retinoic acid receptors during Xenopus tropicalis metamorphosis. Endocrinology. 149(11), 5610-5618.
• Hasebe, T., Kajita, M., Shi, Y.- B., and Ishizuya-Oka, A. (2008) Thyroid hormone-upregulated hedgehog interacting protein is involved in larval-to-adult intestinal remodeling by regulating sonic hedgehog signaling pathway in Xenopus laevis. Dev. Dyn. 237(10), 3006-3015.
• Wang, D., Guo, M.-X., Hu, H.-M., Zhao, Z.-Z., Qiu, H.-L., Shao, H.-J., Zhu, C.-G., Lu, X., Shi, Y.- B., and Li, W.-X. (2008) Human T-cell leukemia virus type 1 oncoprotein tax represses ZNF268 expression through CREB/ATF pathway. J. Biol. Chem. 283(24),16299-308.
• Heimeier, R.A., Hsia, V. S.-C., and Shi, Y.- B. (2008) Participation of BAF57 and BRG1-Containing Chromatin Remodeling Complexes in Thyroid Hormone-Dependent Gene Activation during Vertebrate Development. Mol. Endo. 22(5), 1065-77.

2007

• Matsuda, H., Paul, B. D., Choi, C. Y., and Shi, Y.- B. (2007) Contrasting effects of two alternative splicing forms of coactivator-associated arginine methyltransferase 1 on thyroid hormone receptor-mediated transcription in Xenopus laevis. Mol. Endocrinology. 21(5), 1082-94.
• Sato, Y., Buchholz, D. R., Paul, B. D., and Shi, Y.- B. (2007) A role of unliganded thyroid hormone receptor in postembryonic development in Xenopus laevis. Mechanisms of Development. 124, 476-488.
• Paul, B. D., Buchholz, D. R., Fu, L., and Shi, Y.- B. (2007) SRC-p300 coactivator complex is required for thyroid hormone induced amphibian metamorphosis. J. Biol. Chem. 282, 7472-7481.
• Buchholz, D.R., Heimeier, R.A., Das, B., Washington, T., and Shi, Y.- B. (2007) Pairing morphology with gene expression in thyroid hormone-induced intestinal remodeling and identification of a core set of TH-induced genes across tadpole tissues. Dev. Biol. 303, 576-590.
• Hasebe, T., Hartman, R., Fu, L., Amano, T., and Shi, Y.- B. (2007) Evidence for a cooperative role of gelatinase A and membrane type-1 matrix metalloproteinase during Xenopus laevis development. Mechanisms of Development. 124(1), 11-22.

2006

• Guo, M.-X., Wang, D., Shao, H.-J., Qiu, H.-L., Lu, X., Zhao, Z.-Z., Zhu, C.-G., Shi, Y.- B., and Li, W.-X. (2006) Transcription of Human Zinc Finger 268 Gene Requires an Intragenic Promoter Element. J. Biol. Chem. 281(34), 24623-36.
• Fu, L., Tomita, A., Wang, H., Buchholz, D.R., and Shi, Y.- B. (2006) Transcriptional regulation of the Xenopus laevis stromelysin-3 gene by thyroid hormone is mediated by a DNA element in the first intron. J. Biol. Chem. 281(25), 16870-8.
• Hasebe, T., Hartman, R., Matsuda, H., and Shi, Y.- B. (2006) Spatial and temporal expression profiles suggest the involvement of gelatinase A and membrane type 1 matrix metalloproteinase in amphibian metamorphosis. Cell and Tissue Research 324(1), 105-16.

2005

• Paul, B. D., Fu, L., Buchholz, D. R., and Shi, Y.- B. (2005) Coactivator recruitment is essential for liganded thyroid hormone receptor to initiate amphibian metamorphosis. Mol. Cell. Biol. 25, 5712-5724.
• Amano, T., Kwak, O., Fu, L., Marshak, A., and Shi, Y.- B. (2005) The matrix metalloproteinase stromelysin-3 cleaves laminin receptor at two distinct sites between the transmembrane domain and laminin binding sequence within the extracellular domain. Cell Research 15, 150-159.
• Fu, L., Ishizuya-Oka, A., Buchholz, D. R., Amano, T., Matsuda, H., and Shi, Y.- B. (2005) A causative role of stromelysin-3 in ECM remodeling and epithelial apoptosis during intestinal metamorphosis in Xenopus laevis. J. Biol. Chem. 280:27856-65.
• Amano, T., Fu, L., Marshak, A., Kwak, O., and Shi, Y.- B. (2005) Spatio-temporal regulation and cleavage by matrix metalloproteinase stromelysin-3 implicate a role for laminin receptor in intestinal remodeling during Xenopus laevis metamorphosis. Dev. Dynamics. 234, 190-200.
• Paul, B. D., Buchholz, D. R., Fu, L., and Shi, Y.- B. (2005) Tissue- and gene-specific recruitment of steroid receptor coactivator-3 by thyroid hormone receptor during development. J. Biol. Chem. 280 (29), 27165-27172. JBC Paper of the Week.
• Wang, G.-P., Song, E.-Q., Xie, H.-Y., Zhang, Z.-L., Tian, Z.-Q., Zuo, C., Pang, D.-W., Wu, D.-C., and Shi, Y.-B. (2005) Biofunctionalization of fluorescent-magnetic-bifunctional nanospheres and their applications. Chem. Commun. 34, 4276-4278.
• Buchholz, D. R., Paul, B. D., and Shi, Y.- B. (2005) Gene-specific changes in promoter occupancy by thyroid hormone receptor during frog metamorphosis: Implications for developmental gene regulation. J. Biol. Chem. 280(50), 41222-8.
• Ikuzawa, M., Shimizu, K., Yasumasu, S., Iuchi, I., Shi, Y.- B., and Ishizuya-Oka, A. (2005) Thyroid hormone-induced expression of a bZip-containing transcription factor activates epithelial cell proliferation during Xenopus larval-to-adult intestinal remodeling. Dev. Genes Evol. 216(3), 109-18.

2004

• Buchholz, D. R., Fu, L., and Shi, Y.- B. (2004) Cryopreservation of Xenopus transgenic lines. Molecular Reproduction and Development 67, 65-69.
• Buchholz, D. R., Ishizuya-Oka, A., and Shi, Y.- B. (2004) Spatial and temporal expression pattern of a novel gene in the frog Xenopus laevis: correlations with adult intestinal epithelial differentiation during metamorphosis. Mechanisms of Development: Gene Expression Patterns 4 (3), 321-328.
• Tomita, A., Buchholz, D. R., and Shi, Y.- B. (2004) Recruitment of N-CoR/SMRT-TBLR1 corepressor complex by unliganded thyroid hormone receptor for gene repression during frog development. Mol. Cell. Biol. 24, 3337-3346.
• Amano, T, Fu, L., Sahu, S., Markey, M., and Shi, Y.- B. (2004) Substrate specificity of Xenopus matrix metalloproteinase stromelysin-3. International Journal of Molecular Medicine 14, 233-239.
• Buchholz, D. R., Tomita, A., Fu, L., Paul, B. D., and Shi, Y.- B. (2004) Transgenic analysis reveals that thyroid hormone receptor is sufficient to mediate the thyroid hormone signal in frog metamorphosis. Mol. Cell. Biol. 24, 9026-9037.

2003

• Ritchie, J.W.A., Shi, Y.-B. , Hayashi, Y., Baird, F.E., Muchekehu, R.W., Christie, G.R., and Taylor, P.M. (2003). A role for thyroid hormone transporters in transcriptional regulation by thyroid hormone receptors. Mol. Endocrinol. 17, 653-661.
• Tomita, A., Buchholz, D. R., and Shi, Y.- B. (2003) Fusion protein of retinoic acid receptor a with promyelocytic leukemia protein or promyelocytic leukemia zinc-finger protein recruits N-CoR-TBLR1 corepressor complex to repress transcription in vivo. J. Biol. Chem. 278(33), 30788-30795.
• Buchholz, D. R., Hsia, V. S.-C., Fu, L., and Shi, Y.- B. (2003) A dominant negative thyroid hormone receptor blocks amphibian metamorphosis by retaining corepressors at target genes. Mol. Cell. Biol. 23, 6750-6758.
• Paul, B. D., and Shi, Y.- B. (2003) Distinct expression profiles of transcriptional coactivators for thyroid hormone receptors during Xenopus laevis metamorphosis. Cell Research 13, 459-464.

2002

• Amano, T., Leu, K., Yoshizato, K., and Shi, Y.- B. (2002) Thyroid hormone regulation of a transcriptional coactivator in Xenopus laevis: Implication for a role in postembryonic tissue remodeling. Dev. Dynamics 223, 526-535.
• Fu, L., Buchholz, D., and Shi, Y.- B. (2002) A novel double promoter approach for identification of transgenic animals : a tool for in vivo analysis of gene function and development of gene-based therapies. Molecular Reproduction and Development 62, 470-476.
• Seo, Y.-W., Sanyal, S., Kim, H.-J., Won, D. H., An, J.-Y., Amano, T., Zavacki, A. M., Kwon, H.-B., Shi, Y.- B., Kim, W.-S., Kang, H.-J., Moore, D. D., and Choi, H.-S. (2002). FOR, a Novel Orphan Nuclear Receptor Related to Farnesoid X Receptor. J. Biol. Chem. 277, 17836-17844.
• Hsia, V. S.-C., and Shi, Y.- B. (2002) Chromatin Disruption and Histone Acetylation in the Regulation of HIV-LTR by Thyroid Hormone Receptor. Mol. Cell. Biol. 22, 4043-4052.
• Sachs, L.M., Jones, P. L., Havis, E., Rouse, N, Demeneix, B. A., and Shi, Y.- B. (2002). N-CoR recruitment by unliganded thyroid hormone receptor in gene repression during Xenopus laevis development. Mol. Cell. Biol. 22, 8527-8538.

2001

• Hsia, V. S.-C., Wang, H, and Shi, Y.- B. (2001) Involvement of Chromatin and Histone Acetylation in the Regulation of HIV-LTR by Thyroid Hormone Receptor. Cell Research 11, 8-16.
• Damjanovski, S., Amano, T., Li, Q., Pei, D., and Shi, Y.- B. (2001) Overexpression of Matrix Metalloproteinases Leads to Lethality in Transgenic Xenopus Laevis: Implications for Tissue-Dependent Functions of Matrix Metalloproteinases during Late Embryonic development. Dev. Dynamics 221, 37-47.
• Jones, P. L., Sachs, L. M., Rouse, N., Wade, P. A, and Shi, Y.- B. (2001) Multiple N-CoR complexes contain distinct histone deacetylases. J. Biol. Chem. 276, 8807-8811.
• Sachs, L.M., Amano, T., Rouse, N, and Shi, Y.- B. (2001) Involvement of histone deacetylase at two distinct steps in gene regulation during intestinal development in Xenopus laevis.. Dev. Dynamics 222, 280-291.
• Sachs, L.M., Amano, T., and Shi, Y.- B. (2001) An essential role of histone deacetylases in postembryonic organ transformations in Xenopus laevis. International Journal of Molecular Medicine 8, 595-601.
• Ishizuya-Oka, A., Ueda, S., Inokuchi, T., Amano, T., Damjanovski, S, Stolow, M., and Shi, Y.- B. (2001) Thyroid hormone-induced expression of Sonic hedgehog correlates with adult epithelial development during remodeling of the Xenopus stomach and intestine. Differentiation, 69, 27-37.

2000

• Damjanovski, S., Puzianowska-Kuznicka, M., Ishizuya-Oka, A., and Shi, Y.- B. (2000) Differential regulation of three thyroid hormone-responsive matrix metalloproteinase genes implicates distinct functions during frog embryogenesis. FASEB J. 14, 503-510.
• Ishizuya-Oka, A., Li, Q., Amano, T., Damjanovski, S., Ueda, S., and Shi, Y.- B. (2000) Requirement for matrix metalloproteinase stromelysin-3 in cell migration and apoptosis during tissue remodeling. J. Cell Biol. 150, 1177-1188.
• Urnov, F.D., Yee, J., Collingwood, T.N., Bauer, A, Beug, H., Shi, Y.- B., and Wolffe, A. P. (2000). Targeting of N-CoR-HDAC3 by the oncoprotein v-ErbA yields a chromatin infrastructure-dependent transcriptional repression pathway. EMBO J. 19, 4074-4090.
• Damjanovski, S., Sachs, L.M. and Shi, Y.- B. (2000) Multiple stage-dependent roles for histone deacetylases during amphibian embryogenesis: Implications for the involvement of extracellular matrix remodeling. Int. J. of Dev. Biol. 44, 769-776.
• Sachs, L.M. and Shi, Y.- B. (2000) Targeted chromatin binding and histone acetylation in vivo by thyroid hormone receptor during amphibian development. PNAS 97, 13138-13143.

1999

• Damjanovski, S., Ishizuya-Oka, A., and Shi, Y.- B. (1999) Spatial and temporal regulation of collagenases-3, -4, and stromelysin-3 implicate distinct functions in apoptosis and tissue remodeling during frog metamorphosis.Cell Research, 9, 91-105.
• Vermaak, D., Wade, P. A., Jones, P. L., Shi, Y.- B., and Wolffe, A. P. (1999) Functional Analysis of the SIN3-histone deacetylase RPD3-RbAp48-histone H4 connection in the Xenopus oocyte. Mol. Cell. Biol. 19, 5847-5860.
• Ritchie, J. W. A., Peter, G. J., Shi, Y.- B., and Taylor, P. M. (1999) Thyroid hormone transport by 4F2hc-IU12 heterodimers expressed in Xenopus oocytes. J. Endocrinology. 163, R5-R9.

1998

• Wong, J., Patterton, D., Imhof, D., Guschin, D., Shi, Y.- B., and Wolffe, A. P. (1998) Distinct requirements for chromatin assembly in transcriptional repression by thyroid hormone receptor and histone deacetylase. _EMBO J._17, 520-534.
• Minucci, S., Wong J., Blanco, J., Shi, Y.- B., Wolffe, A. P., and Ozato, K. (1998). Retinoid receptor induced alteration of the chromatin assembled on a ligand responsive promoter in Xenopus oocytes. Molecular Endocrinology 12, 315-324.
• Gao, X., Sedgwick, T., and Shi, Y.- B., Evans, T. (1998). Distinct functions are implicated for the GATA-4/5/6 transcription factors in the regulation of intestine epithelial cell differentiation. Mol. Cell. Biol. 18, 2901-2911.
• Wong, J., Liang, V. C.-T., Sachs, L. M., and Shi, Y.- B. (1998). Transcription from the thyroid hormone dependent promoter of Xenopus laevis TR bA gene requires a novel upstream element and the initiator but not a TATA box. J. Biol. Chem. 273, 14186-14193.
• Li, J., Liang, V. C.-T., Sedgwick, T., Wong, J., and Shi, Y.- B. (1998). Unique organization and involvement of GAGA factors in the transcirptional regulation of the Xenopus stromelysin-3 gene. Nuc. Acids Res. 26, 3018-3025.
• Torrents, D., Estevez, R., Pineda, M., Fernandez, E., Lloberas, J., Shi, Y.- B., Zorzano, A., and Palacin, M. (1998).Identification of a new cDNA (y+LAT-1) that co-expresses system y+L activity with 4F2hc in oocytes: A candidate gene for Lysinuric Protein Intolerance. J. Biol. Chem. 273, 32437-32445.

1997

• Ishizuya- Oka, A., Stolow, M. A., Ueda, S., and Shi, Y.- B. (1997) Temporal and spatial expression of an intestinal Na +/PO 4 3- cotransporter correlates with epithelial transformation during thyroid hormone-dependent frog metamorphosis. Developmental Genetics. 20, 53-66.
• Shi, Y.- B., and Ishizuya-Oka, A. (1997) Auto-activation of Xenopus TR b genes correlates with larval epithelial apoptosis and adult cell proliferation. J. of Biomed. Science. 4, 9-18.
• Denver, R. J., Pavgi, S., and Shi, Y.- B. (1997) Thyroid hormone-dependent gene expression program for Xenopusneural development. J. Biol. Chem. 272, 8179-8188.
• Wong, J., Shi, Y.- B., and Wolffe, A. P. (1997) Determinants of chromatin disruption and transcriptional regulation instigated by the thyroid hormone receptor: Hormone regulated chromatin disruption is not sufficient transcriptional activation. EMBO J. 16, 3158-3171.
• Ishizuya- Oka, A., Ueda, S., and Shi, Y.- B. (1997) Temporal and spatial regulation of a putative transcriptional repressor implicates a role during thyroid hormone-dependent organ transformation. Developmental Genetics. 20, 329-337.
• Su, Y., Shi, Y., and Shi, Y.- B. (1997) Cyclosporin A but not FK506 Inhibits Thyroid Hormone-Induced Apoptosis in Xenopus Tadpole Intestinal Epithelium. FASEB J. 11, 559-565.
• Puzianowska-Kuznicka, M., Damjanovski, S., and Shi, Y.- B. (1997) Both TR and RXR are required to efficiently mediate the effects of thyroid hormone on embryonic development and specific gene regulation in Xenopus laevis. Mol. Cell. Biol. 17, 4738-4749.
• Su, Y., Shi, Y., Stolow, M. A., and Shi, Y.- B. (1997) Thyroid hormone induces apoptosis in primary cell cultures of tadpole intestine: Cell type specificity and effects of extracellular matrix. J. Cell Biol. 139, 1533-1543.
• Wong, J., Li, Q., Levi, B.-Z., Shi, Y.- B., and Wolffe, A. P. (1997) Structural and functional features of a specific nucleosome containing a recognition element for the thyroid hormone receptor. EMBO J. 16, 7130-7145.
• Liang, V. C.-T., Sedgwick, T., and Shi, Y.- B. (1997) Characterization of the Xenopus homolog of an immediate early gene associated with cell activation: Sequence analysis and regulation of its expression by thyroid hormone during amphibian metamorphosis. Cell Research. 7, 179-193.
• Ishizuya-Oka, A., Ueda, S., Damjanovski, S., Li, Q., Liang, V. C.-T., and Shi, Y.- B. (1997) Anteroposterior gradient of epithelial transformation during amphibian intestinal remodeling: Immunohistochemical detection of intestinal fatty acid-binding protein. Dev. Biol. 192, 149-161.

Reviews

2023

• Tanizaki, Y., Shibata, Y., Na, W., Shi, Y.-B. (2023) Cell cycle activation in thyroid hormone-induced apoptosis and stem cell development during Xenopus intestinal metamorphosis. Front. Endocrinol. 14:1184013, 1-8. doi: 10.3389/fendo.2023.1184013

2022

• Paul, B., Sterner, Z.R., Buchholz, D.R., Shi, Y.-B., and Sachs, L.M. (2022) Thyroid and corticosteroid signaling in amphibian metamorphosis. Cells 11:1595, 1-23. https://doi.org/ 10.3390/cells11101595
   
• Tanizaki, Y., Zhang, H., Shibata, Y., and Shi, Y.-B. (2022) 甲状腺ホルモン受容体 α は CDK1 経路の調節を介して 幼生型小腸上皮細胞の細胞死を制御する(Thyroid hormone receptor α controls larval intestinal epithelial cell death by regulating the CDK1 pathway). Comparative Endocrinology 48 (No 175): e0035, 1-3.

2021

• Shi, Y.-B. (2021) Life without thyroid hormone receptor. Endocrinology 162 (4): bqab028, 1–12. doi:10.1210/endocr/bqab028

2019

• Fu, L., Yin, J, and Shi, Y.-B. (2019)Involvement of epigenetic modifications in thyroid hormone-dependent formation of adult intestinal stem cells during amphibian metamorphosis. General and Comparative Endocrinology 271:91-96; doi: 10.1016/j.ygcen.2018.11.012

2018

• Buchholz, and Shi, Y.-B. (2018) Dual function model revised by TRα knockout frogs. General and Comparative Endocrinology. 265:214-218.
• Okada, M., and Shi, Y.-B. (2018) The balance of two opposing factors Mad and Myc regulates cell fate during tissue remodeling. Cell & Bioscience 8:51, 1-9.

2017

• Fu, L., and Shi, Y.-B. (2016) The Sox transcriptional factors: Functions during intestinal development in vertebrates. Semin Cell Dev Biol. 63:58-67.

2016

• Wen, L., and Shi, Y.-B. (2016) Regulation of growth rate and developmental timing by Xenopus thyroid hormone receptor α. Development, Growth & Differentiation 58(1):106-15.
• Sun, G., Roediger, J., and Shi, Y.-B. (2016) Thyroid hormone regulation of adult intestinal stem cells: Implications on intestinal development and homeostasis. Reviews in Endocrine and Metabolic Disorders. 17(4):559-569.

2013

• Gimaldi, A., Buisine, N., Miller, T., Shi, Y.-B., and Sachs, M. L. (2013) Mechanisms of thyroid hormone receptor action during development: Insights from amphibian studies. Biochim Biophys Acta. 1830(7):3882-92.

2012

• Sun, G., and Shi, Y.-B. (2012) Thyroid hormone regulation of adult intestinal stem cell development: Mechanisms and evolutionary conservations. Int. J. Biol. Sci. 8(8):1217-24.

2011

• Shi, Y.-B., Hasebe, T., Fu, L., Fujimoto, K., and Ishizuya-Oka, A. (2011) The development of the adult intestinal stem cells: Insights from studies on thyroid hormone-dependent amphibian metamorphosis. Cell & Bioscience 1:30, 1-9.
• Xue, L., Yi, H., Huang, Z., Shi, Y.-B.*, and Li, W.-X.* (2011) Global Gene Expression during the Human Organogenesis: From Transcription Profiles to Function Predictions. Int. J. Biol. Sci. 7, 1068-1076. (*Corresponding Authors)

2010

• Das, B. Matsuda, H., Fujimoto, K., Sun, G.-H., Matsuura, K., and Shi, Y.-B. (2010) Molecular and genetic studies suggest that thyroid hormone receptor is both necessary and sufficient to mediate the developmental effects of thyroid hormone. General and Comparative Endocrinology. 168, 174-180.
• Heimeier, R.A., and Shi, Y.-B. (2010) Amphibian metamorphosis as a model for studying both the morphological effects and the underlying molecular basis of endocrine disruptors on vertebrate development: A case study with the xenoestrogen bisphenol A. General and Comparative Endocrinology. 168, 181-189.
• Mathew, S., Fu, L., Hasebe, T., Ishizuya-Oka, A., and Shi, Y.-B. (2010) Tissue-dependent induction of apoptosis by matrix metalloproteinase stromelysin-3 during amphibian metamorphosis. Birth Defects Research Part C: Embryo Today. 90(1), 55-66.

2009

• Shi, Y.- B. (2009) Dual functions of thyroid hormone receptors in vertebrate development: the roles of histone-modifying cofactor complexes (The 2008 Van Meter Award Prize Lecture and Review). Thyroid. 19, 987-999. (Cover photo).
• Ishizuya-Oka, A., Hasebe, T., and Shi, Y.-B. (2009) Apoptosis in amphibian organs during metamorphosis. Apoptosis. 15, 350-364.

2008

• Ishizuya-Oka, A, and Shi, Y.- B. (2008) Thyroid-hormone regulation of stem cell development during intestinal remodeling. Molecular and Cellular Endocrinology. 288, 71-78.

2007

• Shi, Y.- B., Fu, L., Hasebe, T., Ishizuya-Oka, A. (2007). Regulation of ECM remodeling and cell fate determination by matrix metalloproteinase stromelysin-3 during thyroid hormone-dependent postembryonic development. Pharmacology & Therapeutics. 116, 391-400.
• Ishizuya-Oka, A, and Shi, Y.- B. (2007) Regulation of Adult Intestinal Epithelial Stem Cell Development by Thyroid hormone during Xenopus laevis Metamorphosis. Dev. Dyn. 236, 3358-3368.
• Fu, L., Hasebe, T., Ishizuya-Oka, A., and Shi, Y.- B. (2007) Roles of matrix metalloproteinases and ECM remodeling during thyroid hormone-dependent intestinal metamorphosis in Xenopus laevis. Organogenesis. 3, 14-19.

2006

• Stewart, D., Tomita, A., Shi, Y.- B., and J. Wong. (2006) Chromatin Immunoprecipitation for studying transcriptional regulation in Xenopus oocytes and tadpoles. Methods Mol Biol. 322, 165-81. (In Xenopus Protocols: Cell Biology and Signal Transdution (Ed. Liu, J.). Humana Press, Inc., Totowa, NJ.)
• Buchholz, D. R., Paul, B. D., Fu, L., and Shi, Y.- B. (2006) Molecular and developmental analyses of thyroid hormone receptor function in Xenopus laevis, the African clawed frog. General and Comparative Endocrinology. 145, 1-19.
• Buchholz, D. R., Paul, B. D., Fu, L., Tomita, A., and Shi, Y.- B. (2006) Molecular and developmental analyses of thyroid hormone receptor function in Xenopus laevis, the African clawed frog. General and Comparative Endocrinology. 145:1-19.

2005

• Wei, L., and Shi, Y.- B. (2005) Matrix metalloproteinase stromelysin-3 in development and pathogenesis. Histology and histopathology. 20:177-85.
• Ishizuya- Oka, A, and Shi, Y.- B. (2005) Molecular mechanisms for thyroid hormone-induced remodeling in the amphibian digestive tract: A model for studying organ regeneration. Dev. Growth Differ. 47(9): 601-607.

2003

• Hsia, V. S.-C., Tomita, A., Obata, K., Paul, B., Buchholz, D., and Shi, Y.- B. (2003). Role of chromatin disruption and histone acetylation in thyroid hormone receptor action: Implications in the regulation of HIV-1 LTR. Histology and histopathology. 18, 323-331.

2002

• Shi, Y.- B., Ritchie, J., and Taylor, P. M. (2002). Complex regulation of thyroid hormone action: Multiple opportunities for pharmacological intervention. Pharmacology & Therapeutics. 94, 235-51.

2001

• Shi, Y.- B., and Ishizuya-Oka, A. (2001). Thyroid hormone regulation of apoptotic tissue remodeling: Implications from molecular analysis of amphibian metamorphosis. Progress in Nucleic Acid Research and Molecular Biology. 65, 53-100.
• Shi, Y.- B., Fu, L. Hsia, V. S.-C., Tomita, A., and Buchholz, D. (2001). Thyroid hormone regulation of apoptotic tissue remodeling during anuran metamorphosis. Cell Research 11, 245-252.

2000

• Sachs, L. M., Damjanovski, S., Jones, P.L., Li, Q., Amano, T., Ueda, S., Shi, Y.- B., and Ishizuya-Oka, S. (2000). Dual function of thyroid hormone receptors during Xenopus development. Comparative Biochemistry and Physiology, Part B. Biochemistry and Molecular Biology. 126, 199-211.
• Wolffe, A. P., Collingwood, T., Li, Q., Yee, J., Urnov, F., and Shi, Y.- B. (2000) Thyroid hormone receptor, v-erbA, and chromatin. Vitamins and Hormones 58, 449-492.
• Damjanovski, S., Amano, T., Li, Q., Ueda, S., Shi, Y.- B., and Ishizuya-Oka, A. (2000) Role of ECM remodeling in thyroid hormone-dependent apoptosis during anuran metamorphosis. Annals of New York Academy of Sciences. 926, 180-191.
• Sachs, L. M., Jones, P. L., Hsia, V. S.-C., and Shi, Y.- B. (2000) Chromatin remodeling and developmental gene regulation by thyroid hormone receptor. Gene Ther Mol Biol 5, 101-109.

1999

• Wolffe, A. P., and Shi, Y.- B. (1999) A hypothesis for the transcriptional control of amphibian metamorphosis by the thyroid hormone receptor. American Zool. 39, 807-817.
• Su, Y., Damjanovski, S., Shi, Y., and Shi, Y.- B. (1999) Molecular and cellular basis of tissue remodeling during amphibian metamorphosis. Histology and histopathology. 14, 175-183.
• Ishizuya- Oka, S., and Shi, Y.- B. (1999). Molecular mechanisms of amphibian intestinal remodeling: Functional implications of thyroid hormone response genes. Protein, Nucleic Acid, and Enzyme (Tanpakushitsu Kakusan Koso). 44, 2060-2068.
• Li, Q., Sachs, L., Shi, Y.- B., and Wolffe, A. P. (1999) Modification of chromatin structure by the thyroid hormone receptor. Trends in Endocrinol. Metabolism. 10, 157-164.

1998

• Shi, Y.- B., Su, Y., Li, Q., and Damjanovski, S. (1998) Auto-regulation of thyroid hormone receptor genes during Metamorphosis: Roles in apoptosis and cell proliferation. Int. J. of Dev. Biol. 42, 107-116.
• Shi, Y.- B., Sachs, L. M., Jones, P. L., Li, Q., and Ishizuya-Oka, A. (1998) Thyroid hormone regulation of Xenopus laevis metamorphosis: Function of TRs and roles of ECM remodeling. Wound Repair and Regeneration. 6, 314-322.
• Shi, Y.- B., Li, Q., Damjanovski, S., Amano, T., and Ishizuya-Oka, A. (1998) Regulation of apoptosis during development: Input from the extracellular matrix. International Journal of Molecular Medicine. 2, 273-282.
• Wade, P. A., Jones, P. L., Vermaak, D., Veenstra, G. J. C., Imhof, A., Sera, T., Tse, C., Ge, H., Shi, Y.- B., Hansen, J. C., and Wolffe, A. P. (1998) Histone deacetylase directs the dominant silencing of transcription in chromatin: Association with MeCP2 and the Mi-2 chromodomain SWI/SNF ATPase. Cold Spring Harbor Symp. Quant. Biol. .63, 435-445.

1997

• Stolow, M. A., Ishizuya-Oka, A., Su, Y., and Shi, Y.- B. (1997) Gene regulation by thyroid hormone during amphibian metamorphosis: Implications on the role of cell-cell and cell-extracellular matrix interactions. American Zoologist. 37, 195-207.
• Shi, Y.- B. (1997) Cell-cell and cell-ECM interactions in epithelial apoptosis and cell renewal during frog intestinal development. Cell Biochemistry and Biophysics. 27, 179-202.
• Wolffe, A. P., Wong, J., Li, Q., Levi, B.-Z., and Shi, Y.- B. (1997) Three steps in the regulation of transcription by the thyroid hormone receptor: establishment of a repressive chromatin, disruption of chromatin and transcriptional activation. Biochem. Soc. Transactions. 25, 612-615.

Book Chapters and Others

2023

• Tanizaki, Y., Bao, L., and Shi, Y.-B. (2023) Steroid-receptor coactivator complexes in thyroid hormone-regulation of Xenopus metamorphosis. In: Gerald Litwack (ed), Hormones and Epigenetics, Vitamins & Hormones 123:483-502. doi: 10.1016/bs.vh.2023.02.003; Academic Press/Elsevier.
• Shi, Y.-B., Tanizaki, Y., Wang, S., and Fu, L. (2023) Essential and subtype-dependent fucntion of Thyroid hormone receptors during Xenopus metamorphosis. In: Gerald Litwack (ed), Hormones Receptors: Structures & Functions, Vitamins & Hormones, 123:503-523. doi: 10.1016/bs.vh.2023.02.004; Academic Press/Elsevier.

2021

• Shi, Y.-B., Shibata, Y., Tanizaki, Y., and Fu, L. (2021) The development of adult intestinal stem cells: Insights from studies on thyroid hormone-dependent anuran metamorphosis. In: Gerald Litwack (ed), Hormones and Stem cells, Vitamins & Hormones, vol. 116:269-293; Academic Press/Elsevier.

2020

• Bao, L., Shi, B., and Shi, Y.-B. (2020) Viewpoint: Intestinal homeostasis: A communication between life and death. Cell & Bioscience 10:66, 1-3; https://doi.org/10.1186/s13578-020-00429-9 .

2019

• Shibata, Y., Bao, L., Fu, L., Shi, B., and Shi, Y.-B. (2019) Functional Studies of Transcriptional Cofactors via Microinjection-Mediated Gene Editing in Xenopus. In: Liu C., Du Y. (eds) Microinjection. Methods in Molecular Biology. 1874:507-524; Humana Press, New York, NY; doi:10.1007/978-1-4939-8831-0_29

2018

• Fu, L., Wen, L., and Shi, Y.-B. (2018) Role of thyroid hormone receptor in amphibian development. In: Michelina Plateroti and Jacques Samarut (eds.), Thyroid Hormone Nuclear Receptor: Methods and Protocols, Methods in Molecular Biology, 1801:247-263; Humana Press, New York, NY. doi:10.1007/978-1-4939-7902-8_20.
• Buchholz, D.R., and Shi, Y.-B. (2018) Methods for Investigating the Larval Period and Metamorphosis in Xenopus. InCold Spring Harb Protoc: Xenopus (Ed.Sive, H.). Cold Spring Harbor Laboratory Press.¿ Cold Spring Harb Protoc 2018(10):pdb.top097667; doi:10.1101/pdb.top097667.

2017

• Yan, H., Shi, Y.-B., and Huang, J.(2017) iPSCs Are Safe. Cell & Bioscience 7:30, 1-2.
• Okada, M., and Shi, Y.-B. (2017) Cell Proliferation Analysis during Xenopus Metamorphosis (Metamorphosis chapter). InCold Spring Harb Protoc: Xenopus (Ed.Sive, H.). Cold Spring Harbor Laboratory Press. pp 696-701; doi:10.1101/pdb.prot097717.
• Shi, Y.-B., and Yin, D. (2017) Research highlight: A good sugar, D-mannose, suppresses autoimmune diabetes. Cell & Bioscience 7:48, 1-2.

2014

• Ma, J., and Shi, Y.-B. (2014) Editorial: The Mesobuthus martensii genome reveals the molecular diversity of scorpion toxins. Cell & Bioscience 4:1, 1-2

2013

• Jin, D.-Y., Shi, Y.-B., and Wu, T.-C. (2013) In Memoriam: Kuan-Teh Jeang, MD PhD (1958-2013). Cell & Bioscience 3:13, 1-3.

2012

• Zhao, K., and Shi, Y.-B. (2012) An anti-cancer Smurf. Cell & Bioscienc e2:10, 1-2
• Shi, Y.-B. (2012) The 2011 Ming K Jeang Award for Excellence in Cell & Bioscience. Cell & Bioscience 2:16, 1.

2011

• Shi, Y.-B. (2011) The right journal for the right time. Cell & Bioscience 1:1, 1.
• Ishizuya-Oka, A., and Shi, Y.-B. (2011) Evolutionary insights into postembryonic development of adult intestinal stem cells. Cell & Bioscience 1:37, 1-3.

2007

• Buchholz, D. R., Paul, B. D., and Shi, Y.- B. (2007) Chromatin immunoprecipitation for in vivo studies of transcriptional regulation during development. In Methods in Signal Transduction: Analysis of Growth Factor Signaling in Embryos (Eds. Whitman, M., and Sater, A. K.) CRC Press, FL. 305-319.

2004

• Ishizuya- Oka, A., Amano, T., Fu, L., and Shi, Y.- B. (2004) Regulation of apoptosis by extracellular matrix during postembryonic development in Xenopus laevis. In When cells die II: A comprehensive evaluation of apoptosis and programmed cell death (Eds. Lockshin, R. A., and Zakeri, Z.). John Wiley & Sons, Inc., New York. 123-141.
• Sang, Q. A., and Shi, Y.- B. (2004) Collagenase 4 (Xenopus). In Handbook of proteolytic enzymes, 2nd Edn. (Eds. A. J. Barrett, N. D. Rawlings, and J. F. Woessner). Academic Press, New York. 494-497.

2003

• Jones, P. L., and Shi, Y.- B. (2003) N-CoR-HDAC corepressor complexes: Roles in transcriptional regulation by nuclear hormone receptors. In Current Topics in Microbiology and Immunology: Protein Complexes that Modify Chromatin (Ed. Workman, J. L.). Springer-Verlag, Berlin. 274, 237-268.
• Amano, T., Fu, L., Ishizuya-Oka, A., and Shi, Y.- B. (2003) Thyroid hormone induced apoptosis during amphibian metamorphosis. In Molecular Mechanisms of Programmed Cell Death. (Eds. Y. Shi, J. Cidlowski, D. Scott, J. Wu, and Shi, Y.- B. ). pp. 9-19. Kluwer Academic/Plenum, New York.

2002

• Damjanovski, S., Sachs, L.M. and Shi, Y.- B. (2002) Function of thyroid hormone receptors during amphibian development. In Methods in Molecular Biology: Thyroid hormone receptors (Ed. Baniahmad, A.). Humana Press, Inc., Totowa, NJ. 202, 153-176.
• *Shi, Y.- B. *(2002) Roles of matrix metalloproteinases in developmental and pathological processes. In Frontiers of Biotechnology and Pharmaceuticals (Eds. Guo, M., Chen, S., Reiner, J., and Zhao, K). Science Press, New York. 3, 46-57.

2000

• Shi, Y.- B. (2000) Temporal and spatial regulation of apoptosis in tissue remodeling: Implications from molecular studies of amphibian development. In Cell Biology and Tumor Immunology (Ed. Y.J. Guo). pp 49-58. Military Medical Science Publication Co., Beijing.

1998

• Shi, Y.- B., and Sang, Q. A. (1998) Collagenase 4 (Xenopus). In Handbook of proteolytic enzymes (Eds. A. J. Barrett, N. D. Rawlings, and J. F. Woessner). pp 1170-1172. Academic Press, New York.

1997

• Shi, Y.- B., and Ishizuya-Oka, A. (1997) Activation of matrix metalloproteinase genes during thyroid hormone-induced apoptotic tissue remodeling. In Programmed Cell Death. (Eds. Shi **Y.- B., Y. Shi, Y. Xu, and D. Scott). pp. 13-26. Plenum Publishing Corp., New York.

Books

• Shi, Y.-B. (2013) Ed. Current Topics in Developmental Biology: Animal Metamoprhosis. Academic Press, an imprint of ELSEVIER INC., Burlington, MA, *** pp.
• Shi, Y.- B., Shi, Y., Xu, Y., and Scott, D. (1997) Eds. Programmed Cell Death. Plenum Publishing Corp., New York, 171 pp.
• Shi, Y.- B. (1999). Amphibian Metamorphosis: From morphology to molecular biology. John Wiley & Sons, Inc., New York, 288pp.
• Shi, Y., Cidlowski, J., Scott, D., Wu, J., and Shi, Y.- B. (2003) Eds. Molecular Mechanisms of Programmed Cell Death. Kluwer Academic/Plenum, New York, 229 pp.