生物資訊核心實驗室

生物資訊核心實驗室

現任委員 Committee Member

研究副技師 Associate Research Specialist

助理 Research Assistant

  • 林詠儀

植物暨微生物學研究所生物資訊核心實驗室設立於2007年初，我們的任務是協助研究人員運用生物資訊專業知識及相關工具。為此，我們提供以下服務：

  1. 諮商：生物資訊軟體及統計方法的使用

  2. 計算：針對使用者的特定問題使用指定軟體進行運算

  3. 研發：客製化並整合不同生物資訊程式，使之穩定運算

  4. 高效能運算：我們協助維護植微所內部高效能運算叢集，請參考相關說明網頁(內部系統連結)以取得更多資訊

  5. 教育訓練：不定時舉辦生物資訊訓練課程，我們的檔案庫(內部系統連結)有所有課程的投影片檔案

諮詢時間
每周五下午一點半到兩點半，我們會在植微大樓R106會議室。如遇所方有其他活動則暫停。其他時間歡迎同仁直接與我們聯繫。歡迎各位同仁前來討論任何生物資訊相關問題。舉凡如何使用Excel處理資料，簡易統計分析，如何使用常用的公開資料庫，或者是生物資訊分析的討論。

服務流程
不需要填寫任何表格。我們需要初步的討論以確定需求並將問題轉換成可解決的形式，請以電子郵件和我們聯絡約定時間討論。歡迎同時在信件中提供問題的相關資訊。

收費標準
收費標準為每人工小時1100元。以下為兩例阿拉伯芥研究課題的收費計時紀錄：

  1. RNAseq：15個40M read樣本，耗時約三個工作天。結果包括differentially expressed gene discovery及alternative-splicing comparisons。

  2. DNAseq：9個50M樣本，耗時約兩個半工作天。結果包括SNP/InDel calling及其註解。

服務紀錄
我們持續以由做中學的方式提供各式服務，過往服務案例類型如下：

  • DNAseq data: Sequence assembly / SNP/InDel detection / T-DNA insertion site detection / Tandem duplication detection / Genome rearrangement detection

SNP-caused premature codon. Data from Dr. Wan-Hsing Cheng’s lab, IPMBSNP-caused premature codon. Data from Dr. Wan-Hsing Cheng’s lab, IPMB

  • RNAseq data: Expression level computation / Sample-sensitive alternative splicing events / Alternative polyadenylation detection / Gene fusion detection / scRNAseq data processing

Condition-sensitive intron retention. Detected in 1% data of NCBI SRA SRP071829. Dr. Majori Matzke’s lab, IPMBCondition-sensitive intron retention. Detected in 1% data of NCBI SRA SRP071829. Dr. Majori Matzke’s lab, IPMB

  • Other NGS analyses: SmallRNA expression level computation / SmallRNA target prediction / ChIPseq data processing

  • Systems biology: Co-expression clustering / PPI network computation / Sequence motif searching / GO enrichment computation / Automatic GO annotation

  • Miscellaneous: Enzyme kinetics computation / Computation of isothermal tiling array probes / iTRAQ data processing / Protein structure and interaction prediction

Applied public software for interaction predictionApplied public software for interaction prediction

參考資料
以下檔案供您參考，或者進行自主學習：

  1. 植微所生物資訊核心介紹，以及中研院院內的計算資源

  2. Using RStudio to write R markdown – a plot making practice

  3. Writing R markdown for enrichment analyses

  4. Online AlphaFold3 structure prediction and offline structure manipulation

  5. DEMOs of protein structure applications

開源專案
我們維護以下開源專案：

  • MACCU (Multi-Array Correlation Computation Utility, https://github.com/wdlingit/maccu/)：計算並比較共表現網路(co-expression network)，進一步推論組織專一之基因模組。

Gautam et al., Plant Physiol 2021. Dr. Wolfgang Schmidt’s lab, IPMBGautam et al., Plant Physiol 2021. Dr. Wolfgang Schmidt’s lab, IPMB

  • RackJ (Read Analysis & Comparison Kit in Java, http://rackj.sourceforge.net/)：根據RNAseq資料，計算基因表現量，並推論與樣本有關之alternative-splicing事件。

An alternative-splicing event detected by RackJAn alternative-splicing event detected by RackJ

  • GOBU (Gene Ontology Browsing Utility, https://gobu.sourceforge.io/)：提供友善的圖形化使用者介面以操作基因本體論資料，包括快速計算富集分析。

Selected Publications

Meyer P, Carpentier S, Mithöfer A, Vélez-Bermúdez IC, Lin WD, Herrera HS, Schmidt W, Schmitz-Linneweber C, and Geilfus CM. (2026) Apoplastic pH modulates gene expression, proteome, and ABA content in Vicia faba guard cells, accompanied by reduced stomatal aperture under salt stress. Journal of experimental botany, erag181. Advance online publication. https://doi.org/10.1093/jxb/erag181

Shrestha R, Reyes AV, Carey S, Karunadasa SS, Zhai W, Byun D, Lin WD, Li J, Alerte K, Cui H, Wang ZY, and Xu SL.(2025) Next-Generation Mapping of the ACINUS-Mediated Alternative Splicing Machinery and Its Regulation by O-glycosylation in Arabidopsis. bioRxiv : the preprint server for biology, 2025.01.04.631329. https://doi.org/10.1101/2025.01.04.631329

Vélez-Bermúdez IC, Lin WD, Chou SJ, Chen AP, and Schmidt W. (2025) Transcriptome and translatome comparison of tissues from Arabidopsis thaliana. Scientific data, 12(1), 504. https://doi.org/10.1038/s41597-025-04805-3

Kanno T, Chiou P, Wu MT, Lin WD, Matzke A, and Matzke M. (2023) A GFP splicing reporter in a coilin mutant background reveals links between alternative splicing, siRNAs, and coilin function in Arabidopsis thaliana. G3 (Bethesda, Md.), 13(10), jkad175. https://doi.org/10.1093/g3journal/jkad175

Huang CK, Lin WD, Wu SH (2022) An improved repertoire of splicing variants and their potential roles in Arabidopsis photomorphogenic development. Genome Biol. 9;23(1):50. https://doi.org/10.1186/s13059-022-02620-2

Hsieh EJ, Lin WD, Schmidt W (2022) Genomically Hardwired Regulation of Gene Activity Orchestrates Cellular Iron Homeostasis in Arabidopsis. RNA Biol. 19(1):143-161. https://doi.org/10.1080/15476286.2021.2024024

Kanno T, Venhuizen P, Wen TN, Lin WD, Chiou P, Kalyna M, Matzke AJM, Matzke M (2018) PRP4KA, a Putative Spliceosomal Protein Kinase, Is Important for Alternative Splicing and Development in Arabidopsis thaliana. Genetics. 210(4):1267-1285. https://doi.org/10.1534/genetics.118.301515

Salazar-Henao JE, Lin WD, Schmidt W (2016) Discriminative gene co-expression network analysis uncovers novel modules involved in the formation of phosphate deficiency-induced root hairs in Arabidopsis. Sci Rep 6:26820. https://doi.org/10.1038/srep26820

Kanno T, Lin WD, Fu JL, Wu MT, Yang HW, Lin SS, Matzke AJ, Matzke M (2016) Identification of Coilin Mutants in a Screen for Enhanced Expression of an Alternatively Spliced GFP Reporter Gene in Arabidopsis thaliana. Genetics 203(4):1709-20. https://doi.org/10.1534/genetics.116.190751

Sasaki T, Kanno T, Liang SC, Chen PY, Liao WW, Lin WD, Matzke AJ, Matzke M (2015) An Rtf2 domain-containing protein influences pre-mRNA splicing and is essential for embryonic development in Arabidopsis thaliana. Genetics 200(2):523-35. https://doi.org/10.1534/genetics.115.176438

Chang CY, Lin WD, and Tu SL. (2014) Genome-Wide Analysis of Heat-Sensitive Alternative Splicing in Physcomitrella patens. Plant physiology, 165(2), 826–840. https://doi.org/10.1104/pp.113.230540

Wu HP, Su YS, Chen HC, Chen YR, Wu CC, Lin WD, and Tu SL. (2014) Genome-wide analysis of light-regulated alternative splicing mediated by photoreceptors in Physcomitrella patens. Genome biology, 15(1), R10. https://doi.org/10.1186/gb-2014-15-1-r10

Liu MJ, Wu SH, Wu JF, Lin WD, Wu YC, Tsai TY, Tsai HL, and Wu SH.. (2013) Translational landscape of photomorphogenic Arabidopsis. Plant Cell. 25:3699-710. https://doi.org/10.1105/tpc.113.114769

Lan P, Li WF, Lin WD, Santi S, and Schmidt W.(2013) Mapping gene activity of Arabidopsis root hairs. Genome Biology. 14:R67. https://doi.org/10.1186/gb-2013-14-6-r67

Rodríguez-Celma J, Lin WD, Fu GM, Abadía J, López-Millán AF, and Schmidt W. (2013) Mutually exclusive alterations in secondary metabolism are critical for the uptake of insoluble iron compounds by Arabidopsis and Medicago truncatula. Plant physiology, 162(3), 1473–1485. https://doi.org/10.1104/pp.113.220426

Kesari R, Lasky JR, Villamor JG, Des Marais DL, Chen YJ, Liu TW, Lin W, Juenger TE, and Verslues PE. (2012) Intron-mediated alternative splicing of Arabidopsis P5CS1 and its association with natural variation in proline and climate adaptation. Proceedings of the National Academy of Sciences of the United States of America, 109(23), 9197–9202. https://doi.org/10.1073/pnas.1203433109

Lin WD, Liao YY, Yang TJ, Pan CY, Buckhout TJ, and Schmidt W. (2011) Coexpression-based clustering of Arabidopsis root genes predicts functional modules in early phosphate deficiency signaling. Plant Physiology. 155:1383-402. https://doi.org/10.1104/pp.110.166520