Ying-Chung Jimmy Lin Professor
Ying-Chung Jimmy Lin
Education:
Ph.D. North Carolina State University, USA 2014
M.S. National Taiwan University, Taiwan 2008
B.S. National Tsing Hua University, Taiwan 2006
email: YCJimmyLin@ntu.edu.tw
Lab: Life Science Building R1136
Tel: 02-33662509
Research Interests
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Xylem development and evolution, Wood formation
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Transcriptional regulatory network
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Single cell and spatial multi-omics
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Software development
Laboratory Introduction
Xylem is the most abundant tissue on Earth. Wood is xylem, and wood formation is a complex developmental process involving cell proliferation of vascular cambium followed by the differentiation of secondary xylem cells. My research centers on dissecting the developmental and evolutionary basis of xylem formation in flowering plants under changing environments. I integrate single-cell and spatial multi-omics technologies to reconstruct cell-type lineages, regulatory networks, and metabolic reprogramming that drive xylem differentiation. By combining cross-species analyses with abiotic stress experiments, my work aims to reveal how xylem development adapts to mechanical and drought challenges while maintaining structural and functional integrity. These insights provide a foundation for understanding the evolution of vascular tissues and offer strategies to enhance stress resilience in woody and perennial crops.
Selected Publications
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Hsieh J.A., Liou P.C., Lin C.C., Dai X., Hu C.W., Wang I.F., Dang J.F., Ho Y.C., Cheng K.W., Xu W., Kuo S.C., Kao C.T., Yang D.X., Wang R., Xiao K., Lin J.S., Hsu C.C., Hsu C.C., Mai T.L., Cheng Y., Tseng M.C., Li W.*, Chen Y.L.*, Lin Y.J.* (2025) Single-cell and spatial multiomics identifies heterogeneous xylem development driven by mechanical stress in Populus. Developmental Cell (* co-corresponding author) (5yr IF=11.4; R/C=2/39(5.2%), DEVELOPMENTAL BIOLOGY).
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Kao C.T., Yang F.W., Wu M.C., Hung T.H., Hu C.W., Chen C.H., Liou P.C., Mai T.L., Chang C.C., Lin T.Y., Chen Y.L.*, Lin Y.J.*, Su J.C.* (2024) Systematic synthesis, identification and application of monolignol pathway metabolites New Phytologist 244: 1143-1167 (* co-corresponding author) (5yr IF=10.3; R/C=12/273(4.4%), PLANT SCIENCES).
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Chen Y.L.*, Hsieh J.A., Kuo S.C., Kao C.T., Tung C.C., Yu J.H., Chang T.H., Ku C., Xie J., Zhang D., Li Q., Lin Y.J.* (2024) Merit of integrating in situ transcriptomics and anatomical information for precision cell annotation and lineage construction in single-cell analyses. Genome Biology 25:85 (* co-corresponding author) (5yr IF=17.4; R/C=5/171(2.92%), GENETICS & HEREDITY).
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Li W.*, Lin Y.J.*, Chen Y.L., Zhou C., Li S., Ridder N., Oliveira D., Zhang L., Zhang B., Wang J.P., Xu C., Fu X., Luo K., Wu A.M., Demura T., Lu M.Z., Zhou Y., Li L., Umezawa T., Boerjan W., Chiang V.L. (2024) Woody Plant Cell Walls: Fundamental and Utilization. Molecular Plant 17: 112-140 (* co-first author) (5yr IF=22.6; R/C=1/239 (0.8%), PLANT SCIENCES).
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Tung C.C., Kuo S.C., Yang C.L., Yu J.H., Huang C.E., Liou P.C., Sun Y.H., Shuai P., Su J.C., Ku C.*, Lin Y.J.* (2023)Single-cell transcriptomics unveils xylem cell development and evolution. Genome Biology 24:3 (IF=18.010; R/C=4/175(2.00%), GENETICS & HEREDITY) (* co-corresponding author).
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Tsai N.C., Hsu T.S., Kuo S.C., Kao C.T., Hung T.H., Lin D.G., Yeh C.S., Chu C.C., Lin J.S., Lin H.H., Ko C.Y., Chang T.H.*, Su J.C.*, and Lin Y.J.* (2021) Large-scale data analysis for robotic yeast one-hybrid platforms and multi-disciplinary studies using GateMultiplex. BMC Biology 19:214 (IF=7.431; R/C=7/93 (7.52%), BIOLOGY) (* co-corresponding author)
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Yeh C.S., Wang Z., Miao F., Ma H., Kao C.T., Hsu T.S., Yu J.H., Hung E.T., Lin C.C., Kuan C.Y., Tsai N.C., Zhou C., Qu G.Z., Jiang J., Liu G., Wang J.P., Li W.*, Chiang V.L.*, Chang T.H.*, Lin Y.J.* (2019) A Novel Synthetic-Genetic-Array Based Yeast One-Hybrid System for High Discovery Rate and Short Processing Time. Genome Research 29, 1343-1351(IF=11.093; R/C=8/174(4.31%), GENETICS & HEREDITY) (* co-corresponding author)
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Li S.*, Lin Y.J.* (co-first author), Wang P., Zhang B., Li M., Chen S., Shi R., Tunlaya-Anukit S., Liu X., Wang Z., Dai X., Yu J., Zhou C., Liu B., Wang J.P., Chiang V.L., Li W. (2019) Histone Acetylation Cooperating with AREB1 Transcription Factor Regulates Drought Response and Tolerance in Populus trichocarpa. Plant Cell 31, 663-686 (IF=8.631; R/C=6/228(2.6%), PLANT SCIENCES).
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Lin Y.J.*, Chen H.*, Li Q.*, Shi R., Tunlaya-Anukit S., Shuai P., Li W., Li H., Sun Y.H., Sederoff R.R., Chiang V.L. (2017). Reciprocal cross-regulation of VND and SND multi-gene TF families in wood formation in Populus trichocarpa. PNAS 114, E9722-E9729 (* co-first author) (IF=9.7; R/C=4/64(6.3%), MULTIDISCIPLINARY SCIENCES).
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Lin, Y., Li, W., Li, Q., Chen, H., Sederoff, R.R., and Chiang, V.L. (2014). A simple improved-throughput xylem protoplast system for studying wood formation. Nature Protocols 9, 2194-2205. (IF= 9.6; R/C=2/79 (2.53%), BIOCHEMICAL RESEARCH METHODS).
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Lin, Y.*, Li, W.*, Sun, Y.H., Kumari, S., Wei, H.R., Li, Q.Z., Tunlaya-Anukit, S., Sederoff, R.R., and Chiang, V.L. (2013). SND1 transcription factor-directed quantitative functional hierarchical genetic regulatory network in wood formation in Populus trichocarpa. Plant Cell 25, 4324-4341. (* Co-first author). (IF=9.6; R/C=4/204 (1.96%), PLANT SCIENCES).
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Li Q.*, Lin Y.* (co-first author), Sun Y. H., Song J., Chen H., Zhang X. H., Sederoff R. R., and Chiang V. L. (2012). Splice variant of the SND1 transcription factor is a dominant negative of SND1 members and their regulation in Populus trichocarpa. PNAS 109, 14699-14704. (IF=9.7; R/C=4/57 (7.01%), MULTIDISCIPLINARY SCIENCES).
Courses Taught
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General Biology
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Phytophysiology
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Protoplast transformation system
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