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Ying-Chung Jimmy Lin Associate 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

 

Specialty: Xylem development and evolution, transcription regulation

email: YCJimmyLin@ntu.edu.tw

Lab: Life Science Building R1136

Tel: 02-33662509

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Research Interests

  1. Xylem development and evolution, Wood formation

  2. Transcriptional regulatory network

  3. Bioinformatics (single cell sequencing, software development)

  4. Cancer biology, drug 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. Growth and development in multicellular organisms are regulated at many levels by transacting molecules following well-structured regulatory hierarchies. Understanding the regulatory hierarchy of wood formation will offer novel and more precise genetic approaches to improve the productivity of forest trees. Using Populus trichocarpa protoplasts from stem-differentiating xylem (SDX) as a model, we have begun to reveal the transcriptional regulatory network involved in secondary cell wall formation.

 

Secondary xylem in woody angiosperms consists of three types of cells, fiber, vessel and ray. In vascular cambium, one layer of stem cells divides and differentiates to give rise to all the three wood cell types. The three types of cells have unique functions. Fiber cells provide support, vessels transport water, and ray cells store nutrients and extractives. Through single cell sequencing and laser capture microdissection, we aim to investigate xylem development through the dissection of individual cell-type development to study the detailed mechanisms.

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Selected Publications

  1. 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).

  2. 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).

  3. 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).

  4. Dai X., Zhai R., Lin J., Wang Z., Meng D., Li M., Mao Y., Gao B., Ma H., Zhang B., Sun Y., Li S., Zhou C., Lin Y.J., Wang J.P., Chiang V.L., Li W. Nature Plants 9: 96–111 (5yr IF=19.328; R/C=4/239(top 1.67%), PLANT SCIENCES).

  5. 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)

  6. 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)

  7. 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).

  8. 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).

  9. 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).

  10. 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).

  11. 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

  • General Biology 　

  • Phytophysiology 　

  • Protoplast transformation system

Photos

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