Profile：Tung, Chein-Yi

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Hi. I am an assistant researcher at the National Yang-Ming University VYM Genome Research Center. I have over ten years experience in genomic tech and data analysis. My works are majorly concentrating on the experimental design of microarray, data analysis, and next generation sequencing.  My research was started from wet-lab, molecular biology, Cell biology and microbiology. After the post-genome era coming, I spend most of my time working on genome study and bioinformatics. My experiences are across both wet-lab and dry-lab. You are welcome to discuss with me and we’ll find a way to solve your problem.

Field:

Genomics, Microarray, Bioinformatics, NGS, Computer programming

Education/Experience：

Education：

Master in Institute of microbiology and immunology, National Yang Ming University, Taipei, Taiwan

PhD in Institute of microbiology and immunology, National Yang-Ming University, Taipei, Taiwan

Experience：

  1. Design, manufacture, evaluation of  first cDNA microarray of VYMGC.
  2. Establishing standard operation protocols and documents of YMGC service.
  3. Developing algorithms for exploring global characteristic in heterogeneous transcriptome datasets.
  4. User service and training of microarray and NGS data analysis.
  5. Developing high-conserved multiple-sequence alignment algorithm(hcMSA) for global bacterial 16S rRNA sequence alignment.
  6. Developing R software package for regulatory-event gene set analysis.

Specialties：

Cell culture and Molecular biology:
Essential cell culture, basic wet-bench work (DNA/RNA isolation, cloning, PCR, RT, real-time quantitative PCR, Southern blot…), high-throughput operation ( liquid handling, array spotting, automated pipeline), basic microscopy (Immune florescence staining, microscope operation)

Genomic technique
Serial analysis of gene expression, microarray pattern design, manufacture, chip processing,

Bioinformatics
Microarray data analysis, gene functional annotation, sequence alignment, biological database management, statistical algorithm.

Programinng and Software

R：event-based Gene Set Analysis Package
C#: Orthologous Sequence Variation Analysis System Ver. 1
JAVA:
1. Orthologous Sequence Variation Analysis System Ver. 2
2. Genome Analyst GUI Workflow System
Other language skill: PHP, SQL, VB and VBA

Publications：

  1. Gelfanov, Y.G. Lai, V. Gelfanova, J.Y. Dong, J.P. Su and N.S. Liao Differential requirement of CD28 costimulation for activation of murine CD8+ intestinal intraepithelial lymphocyte subsets and lymph node cells. J Immunol  155. 76-82. 1995.
  2. Y. Tung, W.N. Lian, Y.J. Chen, C.H. Lin., Changes of transcriptome profiles during hepatic differentiation. poster in 9th HUGO’s Human Genome Meeting, Shanghai, China, 2002.
  3. Y. Tung, C.H. Lin, 功能基因體, 分子檢驗, 303-346, 2003.
  1. Y. Tung, H.F. Haung, W.N. Lian, H.W. Wong, C.H. Lin., Dynamic analyses of gene expression profiles during hepatic differentiation. poster in 11th HUGO’s Human Genome Meeting, Kyoto, Japan, 2005.
  2. H. Jen, T.P. Yang, C.Y. Tung, S.H. Su, C.H. Lin, M.T. Hsu and H.W. Wang, Signature Evaluation Tool (SET): a Java-based tool to evaluate and visualize the sample discrimination abilities of gene expression signatures. BMC Bioinformatics. 2008; 9: 58.
  3. Y. Tung, C.H. Jen, M.T. Hsu, H.W. Wang and C.H. Lin, A novel regulatory event-based gene set analysis method for exploring global functional changes in heterogeneous genomic data sets. BMC Genomics 2009, 10:26.
  4. C Cheng, C.F. Chen, Y.J. Jong, Y. Tung, Y.J. Chen, W.W. Sheng, L.H. Li, S.F. Tsai, M.H. Tsou, Skye H. Cheng, C.M. Chen, Andrew T. Huang, C.H. Lin, M.T. Hsu. (2011) Comparison of genome aberrations between early-onset and late-onset breast cancer. Breast Cancer Cells / Book 5″, ISBN , 979-953-307-184-7
  5. H. Wang, T.H. Hsieh, S.Y. Huang, G.Y. Chau, C.Y. Tung, C.W. Su, J.C. Wu, Forfeited hepatogenesis program and increased embryonic stem cell traits in young hepatocellular carcinoma (HCC) comparing to elderly HCC. BMC Genomics. 2013 Oct 26;14:736.
  6. S. Hsu, C.Y. Tung, C.Y. Yang, C.H. Lin, Response to Stress in Early Tumor Colonization Modulates Switching of CD133-Positive and CD133-Negative Subpopulations in a Human Metastatic Colon Cancer Cell Line, SW620. PLoS One. 2013;8(4):e61133.
  7. Y.Yang, R.H. Lu, C.H. Lin, C.H. Jen, C.Y. Tung, S.H. Yang,J.K. Lin, J.K. Jiang , C.H. Lin. Single nucleotide polymorphisms associated with colorectal cancer susceptibility and loss of heterozygosity in a Taiwanese population. PLoS One. 2014 Jun 26;9(6):e100060.
  8. C. Liang, C.Y. Yang, J.Y. Tseng, H.L. Wang, C.Y. Tung, H.W. Liu, C.Y. Chen, Y.C. Yeh, T.Y. Chou, M.H. Yang, J. Whang-Peng, C.H. Lin.ABCG2 Localizes to the Nucleus and Modulates CDH1 Expression in Lung Cancer Cells. Neoplasia. 2015 Mar;17(3):265-78.

Hi. I am an assistant researcher at the National Yang-Ming University VYM Genome Research Center. I have over ten years experience in genomic tech and data analysis. My works are majorly concentrating on the experimental design of microarray, data analysis, and next generation sequencing.  My research was started from wet-lab, molecular biology, Cell biology and microbiology. After the post-genome era coming, I spend most of my time working on genome study and bioinformatics. My experiences are across both wet-lab and dry-lab. You are welcome to discuss with me and we’ll find a way to solve your problem.

Field:

Genomics, Microarray, Bioinformatics, NGS, Computer programming

Education/Experience：

Education：

Master in Institute of microbiology and immunology, National Yang Ming University, Taipei, Taiwan

PhD in Institute of microbiology and immunology, National Yang-Ming University, Taipei, Taiwan

Experience：

  1. Design, manufacture, evaluation of  first cDNA microarray of VYMGC.
  2. Establishing standard operation protocols and documents of YMGC service.
  3. Developing algorithms for exploring global characteristic in heterogeneous transcriptome datasets.
  4. User service and training of microarray and NGS data analysis.
  5. Developing high-conserved multiple-sequence alignment algorithm(hcMSA) for global bacterial 16S rRNA sequence alignment.
  6. Developing R software package for regulatory-event gene set analysis.

Specialties：

Cell culture and Molecular biology:
Essential cell culture, basic wet-bench work (DNA/RNA isolation, cloning, PCR, RT, real-time quantitative PCR, Southern blot…), high-throughput operation ( liquid handling, array spotting, automated pipeline), basic microscopy (Immune florescence staining, microscope operation)

Genomic technique
Serial analysis of gene expression, microarray pattern design, manufacture, chip processing,

Bioinformatics
Microarray data analysis, gene functional annotation, sequence alignment, biological database management, statistical algorithm.

Programinng and Software

R：event-based Gene Set Analysis Package
C#: Orthologous Sequence Variation Analysis System Ver. 1
JAVA:
1. Orthologous Sequence Variation Analysis System Ver. 2
2. Genome Analyst GUI Workflow System
Other language skill: PHP, SQL, VB and VBA

Publications：

  1. Gelfanov, Y.G. Lai, V. Gelfanova, J.Y. Dong, J.P. Su and N.S. Liao Differential requirement of CD28 costimulation for activation of murine CD8+ intestinal intraepithelial lymphocyte subsets and lymph node cells. J Immunol  155. 76-82. 1995.
  2. Y. Tung, W.N. Lian, Y.J. Chen, C.H. Lin., Changes of transcriptome profiles during hepatic differentiation. poster in 9th HUGO’s Human Genome Meeting, Shanghai, China, 2002.
  3. Y. Tung, C.H. Lin, 功能基因體, 分子檢驗, 303-346, 2003.
  1. Y. Tung, H.F. Haung, W.N. Lian, H.W. Wong, C.H. Lin., Dynamic analyses of gene expression profiles during hepatic differentiation. poster in 11th HUGO’s Human Genome Meeting, Kyoto, Japan, 2005.
  2. H. Jen, T.P. Yang, C.Y. Tung, S.H. Su, C.H. Lin, M.T. Hsu and H.W. Wang, Signature Evaluation Tool (SET): a Java-based tool to evaluate and visualize the sample discrimination abilities of gene expression signatures. BMC Bioinformatics. 2008; 9: 58.
  3. Y. Tung, C.H. Jen, M.T. Hsu, H.W. Wang and C.H. Lin, A novel regulatory event-based gene set analysis method for exploring global functional changes in heterogeneous genomic data sets. BMC Genomics 2009, 10:26.
  4. C Cheng, C.F. Chen, Y.J. Jong, Y. Tung, Y.J. Chen, W.W. Sheng, L.H. Li, S.F. Tsai, M.H. Tsou, Skye H. Cheng, C.M. Chen, Andrew T. Huang, C.H. Lin, M.T. Hsu. (2011) Comparison of genome aberrations between early-onset and late-onset breast cancer. Breast Cancer Cells / Book 5″, ISBN , 979-953-307-184-7
  5. H. Wang, T.H. Hsieh, S.Y. Huang, G.Y. Chau, C.Y. Tung, C.W. Su, J.C. Wu, Forfeited hepatogenesis program and increased embryonic stem cell traits in young hepatocellular carcinoma (HCC) comparing to elderly HCC. BMC Genomics. 2013 Oct 26;14:736.
  6. S. Hsu, C.Y. Tung, C.Y. Yang, C.H. Lin, Response to Stress in Early Tumor Colonization Modulates Switching of CD133-Positive and CD133-Negative Subpopulations in a Human Metastatic Colon Cancer Cell Line, SW620. PLoS One. 2013;8(4):e61133.
  7. Y.Yang, R.H. Lu, C.H. Lin, C.H. Jen, C.Y. Tung, S.H. Yang,J.K. Lin, J.K. Jiang , C.H. Lin. Single nucleotide polymorphisms associated with colorectal cancer susceptibility and loss of heterozygosity in a Taiwanese population. PLoS One. 2014 Jun 26;9(6):e100060.
  8. C. Liang, C.Y. Yang, J.Y. Tseng, H.L. Wang, C.Y. Tung, H.W. Liu, C.Y. Chen, Y.C. Yeh, T.Y. Chou, M.H. Yang, J. Whang-Peng, C.H. Lin.ABCG2 Localizes to the Nucleus and Modulates CDH1 Expression in Lung Cancer Cells. Neoplasia. 2015 Mar;17(3):265-78.

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