Rui Shi

Shi, R., Kernodle, S. P., Steede, T. M., & Lewis, R. S. (2023). Modified physiology of burley tobacco plants genetically engineered to express Yb<sub>1</sub>, a functional EGY enzyme. PLANTA, 258(4). https://doi.org/10.1007/s00425-023-04235-8

Lin, C.-Y., Sun, Y., Song, J., Chen, H.-C., Shi, R., Yang, C., … Chiang, V. L. (2021). Enzyme Complexes of Ptr4CL and PtrHCT Modulate Co-enzyme A Ligation of Hydroxycinnamic Acids for Monolignol Biosynthesis in Populus trichocarpa. FRONTIERS IN PLANT SCIENCE, 12. https://doi.org/10.3389/fpls.2021.727932

Shi, R., Jin, J., Nifong, J. M., Shew, D., & Lewis, R. S. (2021, October 22). Homoeologous chromosome exchange explains the creation of a QTL affecting soil-borne pathogen resistance in tobacco. PLANT BIOTECHNOLOGY JOURNAL. https://doi.org/10.1111/pbi.13693

Jin, J., Shi, R., Lewis, R. S., & Shew, H. D. (2021). RNAseq Reveals Differential Gene Expression Contributing to Phytophthora nicotianae Adaptation to Partial Resistance in Tobacco. AGRONOMY-BASEL, 11(4). https://doi.org/10.3390/agronomy11040656

Dexter-Boone, A., Humphry, M., Shi, R., & Lewis, R. S. (2019). Genetic Control of Facultative Parthenocarpy in Nicotiana tabacum L. JOURNAL OF HEREDITY, 110(5), 610–617. https://doi.org/10.1093/jhered/esz025

Shi, R., Hubert, H., Dexter-Boone, A., Zeng, J., Kernodle, S. P., & Lewis, R. S. (2019). Identification and validation of SNP markers associated with Wz-mediated Phytophthora nicotianae resistance in Nicotiana tabacum L. MOLECULAR BREEDING, 39(7). https://doi.org/10.1007/s11032-019-1015-2

Shi, R., Lewis, R. S., & Panthee, D. R. (2018). Filter paper-based spin column method for cost-efficient DNA or RNA purification. PLOS ONE, 13(12). https://doi.org/10.1371/journal.pone.0203011

Wang, J. P., Matthews, M. L., Williams, C. M., Shi, R., Yang, C., Tunlaya-Anukit, S., … Chiang, V. L. (2018). Improving wood properties for wood utilization through multi-omics integration in lignin biosynthesis. Nature Communications, 9(1), 1579. https://doi.org/10.1038/s41467-018-03863-z

Shi, R., & Panthee, D. R. (2017). A novel plant DNA extraction method using filter paper-based 96-well spin plate. Planta, 246(3), 579–584. https://doi.org/10.1007/s00425-017-2743-3

Lin, Y.-C. J., Chen, H., Li, Q., Li, W., Wang, J. P., Shi, R., … Chiang, V. L. (2017). Reciprocal cross-regulation of VND and SND multigene TF families for wood formation in Populus trichocarpa. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 114(45), E9722–E9729. https://doi.org/10.1073/pnas.1714422114

Shi, R., Wang, J. P., Lin, Y.-C., Li, Q., Sun, Y.-H., Chen, H., … Chiang, V. L. (2017). Tissue and cell-type co-expression networks of transcription factors and wood component genes in Populus trichocarpa. PLANTA, 245(5), 927–938. https://doi.org/10.1007/s00425-016-2640-1

Lin, C.-Y., Li, Q., Tunlaya-Anukit, S., Shi, R., Sun, Y.-H., Wang, J. P., … Chiang, V. L. (2016). A cell wall-bound anionic peroxidase, PtrPO21, is involved in lignin polymerization in Populus trichocarpa. Tree Genetics & Genomes, 12(2). https://doi.org/10.1007/s11295-016-0978-y

Wang, J. P., Chuang, L., Loziuk, P. L., Chen, H., Lin, Y.-C., Shi, R., … Chiang, V. L. (2015). Phosphorylation is an on/off switch for 5-hydroxyconiferaldehyde O-methyltransferase activity in poplar monolignol biosynthesis. Proceedings of the National Academy of Sciences, 112(27), 8481–8486. https://doi.org/10.1073/pnas.1510473112

Li, W., Lin, Y.-C., Li, Q., Shi, R., Lin, C.-Y., Chen, H., … Chiang, V. L. (2014). A robust chromatin immunoprecipitation protocol for studying transcription factor-DNA interactions and histone modifications in wood-forming tissue. NATURE PROTOCOLS, 9(9), 2180–2193. https://doi.org/10.1038/nprot.2014.146

Lin, Y.-C., Li, W., Chen, H., Li, Q., Sun, Y.-H., Shi, R., … Chiang, V. L. (2014). A simple improved-throughput xylem protoplast system for studying wood formation. NATURE PROTOCOLS, 9(9), 2194–2205. https://doi.org/10.1038/nprot.2014.147

Stout, A. T., Davis, A. A., Domec, J.-C., Yang, C., Shi, R., & King, J. S. (2014). Growth under field conditions affects lignin content and productivity in transgenic Populus trichocarpa with altered lignin biosynthesis. BIOMASS & BIOENERGY, 68, 228–239. https://doi.org/10.1016/j.biombioe.2014.06.008

Chen, H.-C., Song, J., Wang, J. P., Lin, Y.-C., Ducoste, J., Shuford, C. M., … Chiang, V. L. (2014). Systems Biology of Lignin Biosynthesis in Populus trichocarpa: Heteromeric 4-Coumaric Acid:Coenzyme A Ligase Protein Complex Formation, Regulation, and Numerical Modeling. The Plant Cell, 26(3), 876–893. https://doi.org/10.1105/tpc.113.119685

Kafle, K., Shi, R., Lee, C. M., Mittal, A., Park, Y. B., Sun, Y.-H., … Kim, S. H. (2014). Vibrational sum-frequency-generation (SFG) spectroscopy study of the structural assembly of cellulose microfibrils in reaction woods. CELLULOSE, 21(4), 2219–2231. https://doi.org/10.1007/s10570-014-0322-3

Chen, H.-C., Song, J., Williams, C. M., Shuford, C. M., Liu, J., Wang, J. P., … Chiang, V. L. (2013). Monolignol Pathway 4-Coumaric Acid: Coenzyme A Ligases in Populus trichocarpa: Novel Specificity, Metabolic Regulation, and Simulation of Coenzyme A Ligation Fluxes. PLANT PHYSIOLOGY, 161(3), 1501–1516. https://doi.org/10.1104/pp.112.210971

Shi, R., Shuford, C. M., Wang, J. P., Sun, Y. H., Yang, Z. C., Chen, H. C., … Chiang, V. L. (2013). Regulation of phenylalanine ammonia-lyase (PAL) gene family in wood forming tissue of Populus trichocarpa. Planta, 238(3), 487–497. https://doi.org/10.1007/s00425-013-1905-1

Min, D., Yang, C., Shi, R., Jameel, H., Chiang, V., & Chang, H. (2013). The elucidation of the lignin structure effect on the cellulase-mediated saccharification by genetic engineering poplars (Populus nigra L. x Populus maximowiczii A.). BIOMASS & BIOENERGY, 58, 52–57. https://doi.org/10.1016/j.biombioe.2013.08.019

Liu, J., Shi, R., Li, Q., Sederoff, R. R., & Chiang, V. L. (2012). A standard reaction condition and a single HPLC separation system are sufficient for estimation of monolignol biosynthetic pathway enzyme activities. PLANTA, 236(3), 879–885. https://doi.org/10.1007/s00425-012-1688-9

Shuford, C. M., Li, Q., Sun, Y.-H., Chen, H.-C., Wang, J., Shi, R., … Muddiman, D. C. (2012). Comprehensive Quantification of Monolignol-Pathway Enzymes in Populus trichocarpa by Protein Cleavage Isotope Dilution Mass Spectrometry. Journal of Proteome Research, 11(6), 3390–3404. https://doi.org/10.1021/pr300205a

Sun, Y.-H., Shi, R., Zhang, X.-H., Chiang, V. L., & Sederoff, R. R. (2012). MicroRNAs in trees. PLANT MOLECULAR BIOLOGY, 80(1), 37–53. https://doi.org/10.1007/s11103-011-9864-z

Shi, R., Yang, C., Lu, S., Sederoff, R., & Chiang, V. L. (2010). Specific down-regulation of PAL genes by artificial microRNAs in Populus trichocarpa. PLANTA, 232(6), 1281–1288. https://doi.org/10.1007/s00425-010-1253-3

Shi, R., Sun, Y.-H., Li, Q., Heber, S., Sederoff, R., & Chiang, V. L. (2010). [Review of Towards a Systems Approach for Lignin Biosynthesis in Populus trichocarpa: Transcript Abundance and Specificity of the Monolignol Biosynthetic Genes]. PLANT AND CELL PHYSIOLOGY, 51(1), 144–163. https://doi.org/10.1093/pcp/pcp175

Jiang, S.-M., Yin, W.-B., Hu, J., Shi, R., Zhou, R.-N., Chen, Y.-H., … Hu, Z.-M. (2009). Isolation of expressed sequences from a specific chromosome of Thinopyrum intermedium infected by BYDV. GENOME, 52(1), 68–76. https://doi.org/10.1139/G08-108

Zhou, R.-N., Shi, R., Jiang, S.-M., Yin, W.-B., Wang, H.-H., Chen, Y.-H., … Hu, Z.-M. (2008). Rapid EST isolation from chromosome IR of rye. BMC PLANT BIOLOGY, 8. https://doi.org/10.1186/1471-2229-8-28

Shi, R., & Chiang, V. L. (2005). Facile means for quantifying microRNA expression by real-time PCR. BIOTECHNIQUES, 39(4), 519–525. https://doi.org/10.2144/000112010

Lu, S. F., Sun, Y. H., Shi, R., Clark, C., Li, L. G., & Chiang, V. L. (2005). Novel and mechanical stress-responsive microRNAs in Populus trichocarpa that are absent from Arabidopsis. Plant Cell, 17(8), 2186–2203. https://doi.org/10.1105/tpc.105.033456

Lu, S. F., Shi, R., Tsao, C. C., Yi, X. P., Li, L. G., & Chiang, V. L. (2004). RNA silencing in plants by the expression of siRNA duplexes. NUCLEIC ACIDS RESEARCH, 32(21). https://doi.org/10.1093/nar/gnh170