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January 27, 2012

Locations of visitors to this page

Education

  • Ph.D. [Aug. 2007 ~ Summer 2012]
    Institute of Bioinformatics, University of Georgia
    (research focus: cellulosic biofuel and cancer informatics)
  • M.S. [Jun. 2002]
    Institute of Cell and Molecular Biology, Taipei Medical University
    (research focus: Vaccinia virus entry)
  • B.S. [Jun. 2000]
    School of Medical Technology, Chung Shan Medical University
    (research focus: gram-negative bacterial protein secretion)

Professional Experience

  • Research Assistant [Aug. 2007 ~ Aug. 2012]
    Computational Systems Biology Laboratory, UGA
  • Research Intern [May 2011 ~ Aug. 2011]
    Eli Lilly, Indianapolis
    (research focus: Functional cancer genomics)
  • Research Assistant [Sep. 2000 ~ Apr. 2007]
    Institute of Molecular Biology & Institute of Information Science, Academia Sinica
    (research focus: Vaccinia virus entry and biomedical text mining)
  • Medical Technologist Trainee [Sep. 1999 ~ Feb. 2000]
    Jen-Ai Hospital, Taiwan

Publications [pubmed]

Papers

  1. "Genome-wide Survey of Recurrent HBV Integration in Hepatocellular Carcinoma" (submitted)
  2. "A gene index and gene expression atlas for gene discovery and characterization in switchgrass" (to be submitted)
  3. "Prokaryotic transcriptional unit identification using RNA-seq data" (to be submitted)
  4. "Clostridium thermocellum Transcriptional Architecture Improvement Using Systems Biology Data and Bioinformatics" (in preparation)
  5. (2011) D. Earl, K. Bradnam, J. St. John, A. Darling, D. Lin, J. Fass, H. On Ken Yu, V. Buffalo, D. R. Zerbino, M. Diekhans, N. Nguyen, P. Nuwantha, A. W.-K. Sung, Z. Ning, M. Haimel, J. T. Simpson, N. A. Fonseca, L. Birol, T. R. Docking, I. Y. Ho, D. S. Rokhsar, R. Chikhi, D. Lavenier, G. Chapuis, D. Naquin,N. Maillet, M. C. Schatz, D. R. Kelley, A. M. Phillippy, S. Koren, S.-P. Yang, W. Wu, W.-C. Chou, A. Srivastava, T. I. Shaw, J. G. Ruby, P. Skewes-Cox, M. Betegon, M. T. Dimon, V. Solovyev, I. Seledtsov, P. Kosarev, D. Vorobyev, R. RamirezGonzalez, R. Leggett, D. MacLean, F. Xia, R. Luo, Z. L, Y. Xie, B. Liu, S. Gnerre, I. MacCallum, D. Przybylski, F. J. Ribeiro, S. Yin, T. Sharpe, G. Hall, P. J. Kersey, R. Durbin, S. D. Jackman, J. A. Chapman, X. Huang, J. L. DeRisi, M. Caccamo, Y. Li, D. B. Jaffe, R. E. Green, D. Haussler, I. Korf, and B. Paten, "Assemblathon 1: A competitive assessment of de novo short read assembly methods", Genome Research. [link]
  6. (2010) P. Dam, I. Kataeva, S.-J. Yang, F. Zhou, Y. Yin, W.-C. Chou, F. L Poole, R. Hettich, R. Gianonne, J. Westpheling, D. L Lewis, R. M Kelly, H. J Gilbert, B. Henrissat, Y. Xu and M. W. W. Adams, "Insights into Plant Biomass to Biofuel Conversion from the Genome Sequence of the Extremely Thermophilic Bacterium Caldicellulosiruptor bescii DSM 6725", Nucleic Acids Research. [pubmed]
  7. (2010) J. Cui, Y. Chen, W.-C. Chou, L. Sun, L. Chen, J. Suo, Z. Ni, M. Zhang, X. Kong, L. L. Hoffman, J. Kang, X. Lv, Y. Su, Y. Gao, H. Zhang, V. Olman, G. Li, D. Johnson, D. W. Tench, I. J. Amster, R. Orlando, D. Puett, F. Li, and Y. Xu, "An integrated transcriptomic and computational analysis for biomarker identification in gastric cancer", Nucleic Acids Research. [pubmed]
  8. (2010) W.-C. Chou, Y. Yin, Y. Xu, "GolgiP: prediction of Golgi resident proteins", Bioinformatics. [pubmed] [GolgiP Website]
  9. (2009) F. Mao, F. Zhou, Y. Yin, W.-C. Chou, C. Zhou, H. Chen, and Y. Xu, "pDAWG: an Integrated Database for Plant Cell-Wall Genes", BioEnergy Research. [SpringerLink] [pDAWG Website]
  10. (2009) I. A. Kataeva, S.-J. Yang, P. Dam, F. L Poole II, Y. Yin, F. Zhou, W.-C. Chou, Y. Xu, L. Goodwin, D. R. Sims, J. C. Detter, L. J. Hauser, J. Westpheling and M. W. W. Adams, "Genome Sequence of the Anaerobic, Thermophilic and Cellulolytic Bacterium Anaerocellum thermophilum DSM 6725", Journal of Bacteriology. [pubmed]
  11. (2009) F. Mao, P. Dam, W.-C. Chou, V Olman, and Y. Xu, "DOOR: a database for prokaryotic operons", Nucleic Acids Research. [pubmed] [Google Scholar] [DOOR Website]
  12. (2007) T.-H. Tsai, W.-C. Chou, Y.-C. Lin, Y.-S. Su, C.-L. Sung, H.-J. Dai, I. T.-H. Yeh, W. Ku, T.-Y. Sung and W.-L. Hsu, "BIOSMILE: A semantic role labeling system for biomedical verbs using a maximum-entropy model", BMC Bioinformatics. [pubmed]
  13. (2006) T.-H. Tsai, S.-H. Wu, W.-C. Chou, Y.-C. Lin, D. He, T.-Y. Sung, and W.-L. Hsu, "Various Criteria in the Evaluation of Biomedical Named Entity Recognition", BMC Bioinformatics. [pubmed]
  14. (2006) T.-H. Tsai, W.-C. Chou, S.-H. Wu, T.-Y. Sung, J. Hsiang, and W.-L. Hsu, "Integrating Linguistic Knowledge into a Conditional Random Field Framework to Identify Biomedical Named Entities", Expert Systems with Applications. [ACM]
  15. (2007) R. T.-H. Tsai, H.-J. Dai, H.-C. Hung, R. T.-K. Lin, W.-C. Chou, Y.-S. Su, M.-Y. Day, and W.-L. Hsu, BESearch: A Supervised Learning Approach to Search for Molecular Event Participants, Proceedings of the IEEE International Conference on Information Reuse and Integration.
  16. (2006) W.-C. Chou, T.-H. Tsai, Y.-S. Su, W. Ku, T.-Y. Sung, and W.-L. Hsu, "A Semi-Automatic Method for Annotating a Biomedical Proposition Bank", ACL Workshop on Frontiers in Linguistically Annotated Corpora 2006. [Google Scholar]
  17. (2006) T.-H. Tsai, W.-C. Chou, Y.-C. Lin, W. Ku, Y.-S. Su, T.-Y. Sung, and W.-L. Hsu, "BIOSMILE: Adapting Semantic Role Labeling for Biomedical Verbs: An Exponential Model Coupled with Automatically Generated Template Features", Proceedings of BioNLP-2006.
  18. (2004) Y.-F. Lin, T.-H. Tsai, W.-C. Chou, K.-P. Wu, T.-Y. Sung, and W.-L. Hsu, "A Maximum Entropy Approach to Biomedical Named Entity Recognition", Proceedings of 4th ACM SIGKDD Workshop on Data Mining in Bioinformatics (BioKDD).
  19. (2004) Y.-F. Lin, W.-C. Chou, K.-P. Wu, T.-Y. Sung, W.-L. Hsu, "InfoMap: A Framework for Integrated Proteomic Knowledge Base", Proceedings of 3rd International Proteomics Conference (IPC04).
  20. (2004) W.-L. Hsu, J.-M. Chang, W.-C. Chou, J.-B. Chen, K.-P. Wu, T.-Y. Sung, C.-F. Chang, W.-J. Wu and T.-H. Huang, "An Iterative Relaxation Technique for the NMR Backbone Assignment Problem", Proceedings of IEEE Fourth Symposium on Bioinformatics and Bioengineering (BIBE2004).

Posters

  1. (2011) W.-C. Chou, H. Zhang, Y. Yin, and Y. Xu, "Bacterial genome sequence finishing with functional genome structure", Genome Informatics Meeting at CSHL.
  2. (2009) Y. Yin, W.-C. Chou, Y. Xu, "Phylogenetic sub-classification of CAZy families and application in identification of novel glycosyl hydrolases in the environmental metagenomes", BioEnergy Science Center 3rd retreat.
  3. (2009) W.-C. Chou, M. Bar-Peled, Y. Xu, "Computational Prediction of Golgi Resident Proteins in Arabidopsis thaliana", Genomics:GTL Awardee Workshop VII.
  4. (2009) W.-C. Chou, M. Bar-Peled, Y. Xu, "Computational Prediction of Golgi Resident Proteins in Arabidopsis thaliana", BioEnergy Science Center 2nd retreat.
  5. (2008) W.-C. Chou, P. Dam, M. Bar-Peled, Y. Xu, "Prediction of Golgi Proteins Based on Structural Domains and Functional Domains", 3rd Annual Computational and Systems Biology Symposium.

Courses taken