Dr. Chang, Yao-Ming 's orcid link picture

Dr. Chang, Yao-Ming

Assistant Research Scientist
  • 2652-3083 (Office)
Specialty:

Computational Biology

Transcriptome Analysis

Gene Regultory Network

Education and Positions:

  • Ph.D. in Computer Science and Information Engeering (National Taiwan Normal University)

As a computational medicine lab, we have been attempting to answer important biomedical questions by developing appropriate methods to analyze data generated from cutting-edge technologies. In recent years, high throughput nucleic acid sequencing technology provides an opportunity to decode the genetic material comprehensively and precisely. Many sequencing technologies (e.g. WGS, RNA-seq, ChIP-seq, ATAC-seq, etc.) had been widely used nowadays. Our research focuses on comparative time-series RNA-seq data which help biologist reveal the dynamics of biological processes and gene regulatory networks. We overcame the challenge in extracting the valuable time information from the series of transcriptomic data by developing a method to construct the time-ordered gene coexpression network (TO-GCN), incorporating gene expression levels, time points, and tissues/conditions altogether.

This method had been applied to different studies, development of human mesenchymal stem cells (MSCs), zebrafish injured heart regeneration, embryonic mouse heart development, human cell line with SARS-CoV-2 infection, etc. Through closely collaborating with different researchers in various projects, we believe this method can help a lot to answer the important but open questions for a long time.

Using the single cell or spatial RNA-seq technology, we are developing a new single cell version of TO-GCN method that can largely improve our analysis resolution to the next (cell-type) level.

Journal 27 Book 0

  1. Huang FL, (Chang YM), Lin CY, Yu SJ, Fu JT, Chou TY, Yeh SW, Liao EC, Li CL* Regulating TKT activity inhibits proliferation of human acute lymphoblastic leukemia cells American journal of cancer research 14(2), 679-695 (2024-02-15) [JCR] [WOS]
  2. Chou Wen-Cheng, Chen Wei-Ting, Kuo Chun-Tse, (Chang Yao-Ming), Lu Yen-Shen, Li Chia-Wei, Hung Mien-Chie, Shen Chen-Yang* Genetic insights into carbohydrate sulfotransferase 8 and its impact on the immunotherapy efficacy of cancer Cell Reports 43(1), 113641 (2024-01-23) [JCR] [WOS]
  3. Siew Jian Jing, Chen Hui-Mei, Chiu Feng-Lan, Lee Chia-Wei, (Chang Yao-Ming), Chen Hung-Lin, Nguyen Thi Ngoc Anh, Liao Hung-Ting, Liu Mengyu, Hagar Hsiao-Tien, Sun Yung-Chen, Lai Hsing-Lin, Kuo Min-Hao, Blum David, Buée Luc, Jin Lee-Way, Chen Shih-Yu, Ko Tai-Ming, Huang Jie-rong, Kuo Hung-Chih, Liu Fu-Tong, Chern Yijuang* Galectin-3 aggravates microglial activation and tau transmission in tauopathy Journal of Clinical Investigation e165523, 1 (2023-11-31) [JCR] [WOS]
  4. Lin Chia-Yeh, (Chang Yao-Ming), Tseng Hsin-Yi, Shih Yen-Ling, Yeh Hsiao-Hui, Liao You-Rou, Tang Han-Hsuan, Hsu Chia-Ling, Chen Chien-Chang, Yan Yu-Ting*, Kao Cheng-Fu* Epigenetic regulator RNF20 underlies temporal hierarchy of gene expression to regulate postnatal cardiomyocyte polarization Cell Reports 42(11), 113416 (2023-11-28) [JCR] [WOS]
  5. Chang Shao-Han, (Chang Yao-Ming), Chen Huan-Yuan, Shaw Fu-Zen, Shyu Bai-Chuang* Time-course analysis of frontal gene expression profiles in the rat model of posttraumatic stress disorder and a comparison with the conditioned fear model Neurobiology of Stress 2352-2895(23), 100569 (2023-09-20) [JCR] [WOS]
  6. Wei Ke-Hsuan, Lin I-Ting, Chowdhury Kaushik, Lim Khai Lone, Liu Kuan-Ting, Ko Tai-Ming, (Chang Yao-Ming), Yang Kai-Chien, Lai Shih-Lei* Comparative single-cell profiling reveals distinct cardiac resident macrophages essential for zebrafish heart regeneration eLife 12, e84679 (2023-07-27) [JCR] [WOS]
  7. Chuang Tzu-Wei, Su Chun-Hao, Wu Pei-Yu, (Chang Yao-Ming), Tarn Woan-Yuh* LncRNA HOTAIRM1 functions in DNA double-strand break repair via its association with DNA repair and mRNA surveillance factors Nucleic Acids Research gkad143, 1 (2023-03-07) [JCR] [WOS]
  8. Weng Yu-Ting, (Chang Yao-Ming), Chern Yijuang* The Impact of Dysregulated microRNA Biogenesis Machinery and microRNA Sorting on Neurodegenerative Diseases International Journal of Molecular Sciences 24(4), 3443 (2023-02-08) [JCR] [WOS]
  9. Hsiang-Chi Huang, Shih-Han Wang, Guo-Chen Fang, Wen-Cheng Chou, Chun-Che Liao, Cheng-Pu Sun, Jia-Tsrong Jan, Hsiu-Hua Ma, Hui-Ying Ko, Yi-An Ko, Ming-Tsai Chiang, Jian-Jong Liang, Chun-Tse Kuo, Te-An Lee, Diego Morales-Scheihing, Chen-Yang Shen, Shih-Yu Chen, Louise D. McCullough, Mi-Hua Tao, Yi-Ling Lin, (Yao-Ming Chang)*, Shu-Ping Wang*, Yun-Ju Lai*, and Chia-Wei Li* Upregulation of PD‐L1 by SARS‐CoV‐2 promotes immune evasion JOURNAL OF MEDICAL VIROLOGY 95(2), e28478 (2023-01-07) [JCR] [WOS]
  10. Yu-Shuen Tsai#, (Yao-Ming Chang)#, Yang-Mooi Lim, Soon-Keng Cheong, I-Fang Chung*, Chee-Yin Wong* Generating transcriptional regulatory networks from time-ordered stem cell differentiation RNA sequencing data STAR Protocols 3(3), 101541 (2022-09-16) [JCR] [WOS]
- More Publications-