Bioinformatics Core Lab

 

Committee Member

 

Associate Research Specialist

 

Research Assistant

  • Yung-I Lin

 

Bioinformatics Core Facility was established in early 2007. The facility has one linux cluster with 10-nodes. With this high performance computation hardware, the facility is capable of providing bioinformatics services using the software tools based on statistics, mathematics and data mining theory for a wide range such as gene and protein sequence analysis, microarray analysis and phylogenetic analysis. The facility also provides bioinformatics consultations and education services to the institute.

In addition to providing bioinformatics services using existing tools, this core facility is dedicated to providing R&D services that fulfill wet labs’ up-to-date requests. Accordingly, we created and/or maintained the following open-source projects under a close collaboration with wet labs of the IPMB.。

MACCU(Multi-Array Correlation Computation Utility, http://maccu.sourceforge.net/):Computation of co-expression networks and comparisons between networks which help finding tissue-specific co-expression modules.

RackJ (Read Analysis & Comparison Kit in Java, http://rackj.sourceforge.net/):In addition to computation of RPKM values of RNAseq data, this toolkit computes read numbers for every exon, intron, and splicing junction, thus enables finding of sample-sensitive alternative-splicing events.

GOBU (Gene Ontology Browsing Utility, http://gobu.openfoundry.org/): A user-friendly graphical interface for GO data manipulation, including fast computation modules for enrichment analysis.

Hardware

1UTwin Cluster ( 10-nodes )

Selected Publications

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.

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. 

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. 

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.

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.