生物資訊核心實驗室

現任委員:

 

研究助技師:

 

助理:

  • 林詠儀

生物資訊核心實驗室設立於2007年初。本實驗室擁有一套10節點的LINUX CLUSTER。透過高效能運算硬體配備,本實驗室提供生物資訊運算服務:使用基於統計,數學及資料探勘理論所發展出來的軟體工具,廣泛地應用在生物相關的研究及應用上,如基因及蛋白質序列分析,微陣列分析及親緣分析等。本實驗室也為本所提供生物資訊相關諮詢及教育訓練服務。

        除了利用現有工具提供生物資訊服務,針對生物實驗室的最新需求,本實驗室也專注於提供研發服務。因此,在與生物實驗室密切合作之下,我們開發或維護了以下開放源碼專案。

  1. MACCU (Multi-Array Correlation Computation Utility, http://maccu.sourceforge.net/): 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。

  1. 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。

  1. GOBU (Gene Ontology Browsing Utility, http://gobu.openfoundry.org/): 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。

設備

        Linux電腦叢集(10節點)

 

Selected Publications (2007-2013)

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. 162:1473-85.

Li W, Lin WD, Ray P, Lan P, and Schmidt W. (2013) Genome-wide detection of condition-sensitive alternative splicing in Arabidopsis roots. Plant Physiology. 162:1750-63.

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.

Lan P, Li WF, Lin WD, Santi S, and Schmidt W. (2013) Mapping gene activity of Arabidopsis root hairs. Genome Biology. Genome Biology. 14:R67.

Chen YT, Shen CH, Lin WD, Chu HA, Huang BL, Kuo CI, Yeh KW, Huang LC, and Chang IF. (2013) Small RNAs of Sequoia sempervirens during rejuvenation and phase change. Plant Biology. 15:27-36.

Sharma S, Lin WD, Villamor JG, and Verslues PE. (2013) Divergent low water potential response in Arabidopsis thaliana accessions Landsberg erecta and Shahdara. Plant Cell & Environment 36: 994-1008.

Chen YC, Chen YC, Lin WD, Hsiao CD, Chiu HW, and Ho JM. (2012) Bio301: A Web-based EST annotation pipeline that facilitates functional comparison studies. ISRN Bioinformatics. (doi:10.5402/2012/139842)

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.