The long-term research goal of our laboratory is to utilize bioinformatic tools/databases in elucidating molecular and cellular aspects of tumor progression and host-tumor immune responses. Our research efforts are intended to elucidate tumor biology and immunology using bioinformatics data-mining knowledge. Current major projects involve:
PTKs are a major class of oncogenes and may serve as useful biomarkers for human cancers. We have established a RAGE PTK profile method combines the RT-PCR/degenerate-primers approach and the differential display approach. With fluorescent labeled primers and capillary electrophoresis, we have achieved high throughput analysis and better QC and QA performance for detecting PTK expression in human cancers.
Our laboratory has devoting much effort to develop bioinformatic tools for studying gene expression transcripts. Previously, we have used the human dbEST database for the discovery of human genes. We have discovered NAGNAG-based tandem repeat would appear to be the major wobble-splicing InDel isoform observed in EST data-mining. We are examining the detailed wobble-splicing mechanism in cells.
An increasing body of evidence has shown that miRNAs function not only during development but also in disease progression. We have now established a new scanning method using criteria based on the features of known human pre-miRNAs to discriminate miRNAs from random sequences. Currently, we have extended our miRNA discovery pipeline to pathogenic viruses and parasites. We have also engaged in the regulation features of human miRNAs in development and diseases.
Selected Recent Publication
Kao HW, Chen HC, Kung HJ, and Lin WC: Tyrosine-Kinase Expression Profiles in Human Gastric Cancer Cell Lines and Their Modulations with Retinoic Acids. British Journal of Cancer 2003, 88: 1058-1064.
LeeI Y, Ho JM, Lin WC: An Algorithm for Generating Representative Functional Annotations Based on Gene Ontology. DEXA Workshops 2003: pp.10-15.
Lai CH, Hu LY, and Lin WC: Single Amino-acid InDel Variants Generated by Alternative Tandem Splice-donor and -acceptor Selection. Biochem. Biophys. Research Communication 2006, 342: 197-205.
Wu CW, Kao HL, Li AFY, Chi CW, and Lin WC: Protein Tyrosine-phosphatase Expression Profiling in Gastric Cancer Tissues. Cancer Letters 2006,242: 95-103.
Li SC, Pan CY, and Lin WC: Bioinformatic Discovery of MicroRNA Precursors from Human ESTs and Introns. BMC Genomics 2006, 7: 164.
Tsai KW and Lin WC: Quantitative Analysis of Wobble Splicing Indicates It Is Not Tissue Specific. Genomics 2006, 88: 855-864.
Hu LY, Tepper CG, Lo SH and Lin WC: An Efficient Strategy to Identify Early TPA-responsive Genes during Differentiation of HL-60 Cells. Gene Expression 2006, 13: 179-189.
Li SC, Tang P and Lin WC: Intronic MicroRNA: Discovery and Biological implications. DNA and Cell Biology 2007, 26: 195-207.
Tsai KW, Tarn WY and Lin WC: Analyzing Wobble Splicing Reveals that BPS-to-NAGNAG Region Contributes to 3`-tandem Acceptor Site Selection. Molecular and Cellular Biology 2007, 27: 5835-5848.
Ho MR, Jang WJ, Chen CH, Ch'ang LY, Lin WC: Designating eukaryotic orthology via processed transcription units. Nucleic Acids Res 2008, 36:3436-3442
Li SC, Shiau CK, Lin WC: Vir-Mir db: prediction of viral microRNA candidate hairpins. Nucleic Acids Res 2008, 36:D184-189
Tsai KW, Kao HW, Chen HC, Chen SJ, Lin WC: Epigenetic control of the expression of a primate-specific microRNA cluster in human cancer cells. Epigenetics 2009, 4:587-592
Li SC, Chan WC, Hu LY, Lai CH, Hsu CN, Lin WC: Identification of homologous microRNAs in 56 animal genomes. Genomics 2010, 96:1-9
Ho MR, Tsai KW, Chen CH, Lin WC: dbDNV: a resource of duplicated gene nucleotide variants in human genome. Nucleic Acids Res 2011, 39:D920-925