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生物資訊研究室

TEL: +886-2-2871-2121 #85204

E-mail: [email protected]

主持人:蔡秉興

2004 ~ 2006  國立清華大學 生物資訊與結構生物碩士

2010 ~ 2016  國立陽明大學 藥理所博士

2016 ~ 2021  台北榮總 醫研部博士後研究員

2021 ~ present台北榮總 醫研部 契約高級助理研究員

《研究室簡介》

生物資訊研究室致力於整合高通量定序數據分析與臨床轉譯研究,運用先進的計算生物學方法,為院內各科部精準醫學研究提供專業的生物資訊分析支援。本研究室結合單細胞轉錄體學、反捲積分析及類器官研究等前沿技術,協助臨床與基礎研究團隊從複雜的基因體數據中挖掘疾病機制與潛在治療標靶。我們的使命是透過計算生物學的專業能力,加速轉譯醫學研究的進程,從數據到知識、從知識到臨床應用,為病患帶來更精準的診斷與治療方案。

《研究興趣》

單細胞測序分析

反卷積RNA-seq

多組學整合:結合轉錄組、蛋白質組與代謝組分析

基因變異與疾病風險:GWAS研究基因多態性對疾病或藥物易感性的影響

核心技術平台

技術領域

技術內容與應用

單細胞定序分析

10x Genomics Cell Ranger pipeline 建置、Seurat/Scanpy 分析流程、細胞類型註解、軌跡分析 (Monocle3)、細胞間通訊分析 (CellChat)

反捲積分析

從 bulk RNA-seq 數據推估腫瘤微環境細胞組成,支援免疫治療研究與預後分析

類器官轉錄體分析

Patient-specific organoid 基因表現特徵解析、藥物反應預測、疾病建模數據整合

NGS 數據處理

RNA-seq、ATAC-seq、WES/WGS 數據品質控管、比對、定量與下游分析

分析服務項目

服務類型

服務說明

差異表現分析

DESeq2、edgeR、limma-voom 差異基因分析,多組別比較與批次校正

路徑富集分析

GSEA、GO/KEGG enrichment、GSVA、Reactome 路徑分析

細胞類型註解

Reference-based annotation、Marker gene analysis、Automated cell typing

視覺化與報告

Publication-ready figures 製作、互動式數據視覺化、分析報告撰寫

數據整合分析

多組學數據整合、公開數據庫挖掘 (GEO、TCGA)、跨平台數據整合

軟硬體資源

高效能計算工作站,支援大規模單細胞數據分析與機器學習運算

合作與服務流程

1. 初步諮詢:討論研究目標與數據類型

2. 方案設計:擬定分析策略與時程

3. 數據分析:執行分析並進行品質控管

4. 成果呈現:提供分析報告與視覺化結果

《未來研究方向》

生物資訊/單細胞基因定序分析/次世代定序資料分析/精準醫學

《執行計畫》

台北榮總院內計畫

  • 計畫名稱: 人類誘導多能幹細胞衍生肝臟模型中TRAF家族對肝炎病毒感染的研究
  • 計畫編號: V111B-022

嚴慶齡計畫

  • 計畫名稱: 囊胚體的擬時基因表現軌跡分析,以鑑定多能幹細胞分化早期肝細胞的發育軌跡
  • 計畫編號: CI-111-23
《獲獎》

2013 東洋生技獎學金

2014 施再嶔神經再生獎學金

2014 台灣藥理學會杜聰明博士研究生論文獎

2019 台灣藥理學會杜聰明博士年輕學者獎

2019科技部博士後研究人員學術研究獎

2021 科技部未來科技獎

2025 中華醫學會SCI優良醫學論文 盧致德院長獎

《受邀演講》

1. 2024 大數據中心 這就是我要的AI GWAS

“從疾病風險相關論文瞭解GWAS基因分析技術的實戰應用”

2. 2024大數據中心 全基因體關聯性分析工作坊

“工作坊-2: Plink 軟體使用”

3. 2023/11/22大數據中心《Big Data+》系列講座:『大數據實戰分享:大師成長之路』之六:

“實戰基因大數據(二):次世代高通量基因定序分析平台於疾病基因體之應用”

4. 2021/10/16 2nd Joint UTAR-UST Symposium on Cancer and Stem Cell Research

“Ash2l interacts with Oct4-stemness circuitry to enhance super-enhancer-driven pluripotency”

《近期研究著作》

* Equal contribution

  1. Ping-Hsing Tsai, Yi-Ping Yang, Chia-Hao Wang, Kung-Hao Liang, Chih-Ling Yeh, Tzu-Yu Huang, Tzyh-Chang Hwang, Wen-Liang Lo, Yuan-Tzu Lan, Lo-Jei Ching, Mong-Lien Wang, Teh-Ia Huo, Yung-Hung Luo, Shih-Hwa Chiou, Shih-Jie Chou (2025, Oct). Multimodal single-cell transcriptomics with patient-specific iPSC-derived airway organoids as a drug screening approach for cystic fibrosis with nonsense mutations. Biomed Pharmacother. 191:118476. (JCR impact factor: 7.5)
  2. Min-Jia Hsieh, Ping-Hsing Tsai, Pin-Hsuan Chiang, Zih-Kai Kao, Zi-Qing Zhuang, Ai-Ru Hsieh, Hsiang-Ling Ho, Shih-Hwa Chiou, Kung-Hao Liang, Yu-Chun Chen (2024, Dec). Genomic insights into mRNA COVID-19 vaccines efficacy: Linking genetic polymorphisms to waning immunity. Human Vaccines & Immunotherapeutics, 20(1):2399382. (JCR impact factor: 4.1). #北榮第一篇TPMI
  3. La'ah AS, Tsai PH, Yarmishyn AA, Ching LJ, Chen CY, Chien Y, Chen JC, Tsai ML, Chen YC, Ma C, Hsu PK, Luo YH, Chen YM, Chiou GY, Lu KH, Lin WC, Chou YT, Wang ML, Chiou SH. (2024, Oct). Neutrophils Recruited by NKX2-1 Suppression via Activation of CXCLs/CXCR2 Axis Promote Lung Adenocarcinoma Progression. Advanced science, e2400370. (JCR impact factor: 14.3)
  4. Ping-Hsing Tsai, Jun-Ren Sun, Yueh Chien, Man Sheung Chan, Winnie Khor, Hsin-Chou Yang, Chih-Heng Huang, Chia- Ni Hsiung, Teh-Yang Hwa, Yi-Ying Lin, Chih-Ling Yeh, Mong-Lien Wang, Yi-Ping Yang, Yuh-Min Chen, Fu-Ting Tsai, Meng-Shiue Lee, Yun-Hsiang Cheng, Shan-Ko Tsai, Ping-Cheng Liu, Shih-Jie Chou, Shih-Hwa Chiou (2024, Jun). Modifications of lipid pathways restrict SARS-CoV-2 propagation in human induced pluripotent stem cell-derived 3D airway organoids. Journal of Advanced Research, 60:127-140. (JCR impact factor: 11.4)
  5. Ya-Chi Yang, Yueh Chien, Aliaksandr A Yarmishyn, Lee-Yieng Lim, Hao-Yu Tsai, Wen-Chuan Kuo, Ping-Hsing Tsai, Sheng-Hsien Yang, Shao-I Hong, Shih-Jen Chen, De-Kuang Hwang, Yi-Ping Yang, Shih-Hwa Chiou (2024, Jun). Inhibition of oxidative stress-induced epithelial-mesenchymal transition in retinal pigment epithelial cells of age-related macular degeneration model by suppressing ERK activation. Journal of Advanced Research, 60:141-157. (JCR impact factor: 11.4)
  6. Jia-Horung Hung, Ping-Hsing Tsai, Wilson Jr F. Aala, Chao-Chung Chen, Shih-Hwa Chiou, Tak-Wah Wong, Kuen-Jer Tsai, Sheng-Min Hsu, Li-Wha Wu (2024, Apr). TIMP3/Wnt axis regulates gliosis of Müller glia. Biochimica et Biophysica. Acta (BBA) - Molecular Basis of Disease, 1870(4):167087. (JCR impact factor: 4.2)
  7. Hsiao-Jung Kao, Ting-Yi Lin, Feng-Jen Hsieh, Jia-Ying Chien, Erh-Chan Yeh, Wan-Jia Lin, Yi-Hua Chen, Kai-Hsuan Ding, Yu Yang, Sheng-Chu Chi, Ping-Hsing Tsai, Chih-Chien Hsu, De-Kuang Hwang, Hsien-Yang Tsai, Mei-Ling Peng, Shi-Huang Lee, Siu-Fung Chau, Chen Yu Chen, Wai-Man Cheang, Shih-Jen Chen, Pui-Yan Kwok, Shih-Hwa Chiou, Mei-Yeh Jade Lu, Shun-Ping Huang (2024, Jan). Highly efficient capture approach for the identification of diverse inherited retinal disorders. npj genomic medicine, 9(1):4. (JCR impact factor: 7.355)
  8. Afeez Adekunle Ishola, Chian-Shiu Chien, Yi-Ping Yang, Yueh Chien, Aliaksandr A Yarmishyn, Ping-Hsing Tsai, Jerry Chieh-Yu Chen, Po-Kuei Hsu, Yung-Hung Luo, Yuh-Min Chen, Kung-Hao Liang, Yuan-Tzu Lan, Teh-Ia Huo, Hsin-I Ma, Ming-Teh Chen, Mong-Lien Wang, Shih-Hwa Chiou (2022, Jan). Oncogenic circRNA C190 Promotes Non-Small Cell Lung Cancer via Modulation of the EGFR/ERK Pathway. Cancer Res, 82(1):75-89. (JCR impact factor: 12.701)
  9. Teh-Ia Huo, Shu-Yein Ho, Ping-Hsing Tsai (2021, May). Post hepatitis B-eliminated hepatocellular carcinoma: New challenges. Liver Int, 41(5):1173-1174. (JCR impact factor: 6.0)
  10. Chian-Shiu Chien, Julie Yi-Shuan Li, Yueh Chien, Mong-Lien Wang, Aliaksandr A Yarmishyn, Ping-Hsing Tsai, Chi-Chang Juan, Phu Nguyen, Hao-Min Cheng, Teh-Ia Huo, Shih-Hwa Chiou, Shu Chien (2021, Feb). METTL3-dependent N 6- methyladenosine RNA modification mediates the atherogenic inflammatory cascades in vascular endothelium. Proc Natl Acad Sci U S A, 118(7):e2025070118. (JCR impact factor: 9.4)
  11. Ping-Hsing Tsai, Yueh Chien, Mong-Lien Wang, Chih-Hung Hsu, Benoit Laurent, Shih-Jie Chou, Wei-Chao Chang, Chian-Shiu Chien, Hsin-Yang Li, Hsin-Chen Lee, Teh-Ia Huo, Jui-Hung Hung, Chung-Hsuan Chen, Shih-Hwa Chiou (2019, Nov). Ash2l interacts with Oct4-stemness circuitry to promote. super-enhancer-driven pluripotency network. Nucleic Acids Research, 47(19):10115-10133. (JCR impact factor: 16.7)
  12. Tsai PH, Wang ML, Chang JH, Yarmishyn AA, Nhi Nguyen PN, Chen W, Chien Y, Huo TI, Mou CY, Chiou SH. (2019, Jun). Dual Delivery of HNF4α and Cisplatin by Mesoporous Silica Nanoparticles Inhibits Cancer Pluripotency and Tumorigenicity in Hepatoma-Derived CD133-Expressing Stem Cells. ACS Appl Mater Interfaces., 11(22):19808-19818. (JCR impact factor: 8.5)

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