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  Shieh Lab

 

 

 

 

 

    

Publications

Referred Journal Papers

  • Yuan, S., Chen, Y. C., Tsai, C. H., Chen, H. W., & Shieh, G. S. (2023), "Feature selection translates drug response predictors from cell lines to patients", Frontiers in Genetics, 14. pdf
  • Tripathi YM, Chatla SB, Chang Y-CI, Huang L-S, Shieh GS (2022) A nonlinear correlation measure with applications to gene expression data. PLoS ONE 17(6): e0270270. https://doi.org/10.1371/journal.pone.027027 pdf
  • Shieh, G. S. (2022). Harnessing Synthetic Lethal Interactions for Personalized Medicine. Journal of Personalized Medicine, 12(1), 98. pdf
  • Hui-Ching Wang, Chien-Jung Chiang, Ta-Chih Liu*, Chun-Chieh Wu, Yi-Ting Chen, Jan-Gowth Chang and Grace S. Shieh* (2021), "Immunohistochemical expression of five protein combinations revealed as prognostic markers in Asian oral cancer", Frontiers in genetics, 12. pdf
  • Tomoaki Imoto*, Grace S. Shieh* and Kunio Shimizu (2020), "Discrete Circular Distributions with Applications to Shared Orthologs of Paired Circular Genomes," CMES, 123(3), pp. 1131-1149. pdf
  • Yu-Chin Hsu, Yu-Ting Hsiao, Tzu-Yuan Kao, Jan-Gowth Chang+ and Grace S. Shieh* (2017), "Detection of Somatic Mutations in Exome Sequencing of Tumor-only Samples", Scientific Reports, 7(1), pp. 15959-. pdf
  • Jan-Gowth Chang+, Chia-Cheng Chen+, Yi-Ying Wu+, Ting-Fang Che, Yi-Syuan Huang, Kun-Tu Yeh, Grace S. Shieh* and Pan-Chyr Yang (2016), " Uncovering synthetic lethal interactions for therapeutic targets and predictive markers in lung adenocarcinoma", Oncotarget, 7(45), pp. 73664-73680. pdf
  • Jau-Chung Hwang, Wen-Wei Sung, Hung-Pin Tu, Kun-Chou Hsieh, Chung-Min Yeh, Chih-Jung Chen, Hui-Chun Tai, Chao-Tien Hsu, Grace S. Shieh, Jan-Gowth Chang, Kun-Tu Yeh*, Ta-Chih Liu* (2015), "The overexpression of FEN1 and RAD54B may act as independent prognostic factors of lung adenocarcinoma", PLOS ONE, 10(10), e0139435. DOI:10.1371/journal.pone.0139435. pdf
  • Khong-Loon Tiong+ , Kuo-Ching Chang+, Kun-Tu Yeh+, Ting-Yuan Liu, Jia-Hong Wu, Ping-Heng Hsieh, Shu-Hui Lin, Wei-Yun Lai, Yu-Chin Hsu, Jeou-Yuan Chen, Jan-Gowth Chang* and Grace S. Shieh* (2014), "CSNK1E/CTNNB1 are synthetic lethal to TP53 in colorectal cancer and are markers for prognosis", NEOPLASIA. pdf
  • Jia-Hong Wu+, Yun-Ju Sun+, Ping-Heng Hsieh and Grace S. Shieh* (2013), "Inferring coregulation of transcription factors and microRNAs in breast cancer", GENE, 518(1), pp. 139-144. pdf
  • Ci-Ren Jiang, Ying-Chao Hung, Chung-Ming Chen and Grace S Shieh* (2012), "Inferring Genetic Interactions via A Data-driven Second Order Model", Frontiers in Statistical Genetics and Methodology, 3(71), pp. 1-10. pdf
  • Wen-Hung Hunag, Grace S. Shieh and Feng-Sheng Wang* (2012), "Optimization of fed-batch fermentation using mixture of sugars to produce Ethanol," Journal of the Taiwan Institute of Chemical Engineers, 43(1), pp. 1-8. (SCI) pdf
  • Jeng-Wei Lu+, Shia Yu+, Wan-Yu Yang, Yu-I Lin, Chao-Chin Li, Ting-Fen Tsai, Ko-Wei Chang, Grace S. Shieh, Shih-Feng Tsai, Horng-Dar Wang and Chiou-Hwa Yuh* (2012), "Identification of the common regulators for hepatocellular carcinoma induced by hepatitis B virus X antigen in a mouse model", Carcinogenesis, pp.1-11. (SCI) pdf
  • Grace S. Shieh, et al.(2011), "H2B ubiquitylation is part of chromatin architecture that marks exon-intron structure in budding yeast", BMC Genomics, 12(627), pp. 1-14. (SCI) pdf
  • G.S. Shieh*, Shurong Zheng, Richard A. Johnson, Yi-Feng Chang, Kunio Shimizu, Chia-Chang Wang and Sen-Lin Tang. (2011), "Modeling and comparing the organization of circular genomes", Bioinformatics, 27(7), pp. 912-918. (SCI) pdf
  • Wen-Hung Wang, Grace S. Shieh and Feng-Sheng Wang* (2010), "Run-to-run optimization of fed-batch fermentation for ethanol production", Chemical Engineering & Technology , 33(9), pp. 1488-1494. (SCI) pdf
  • C.M. Chen+, Chih Lee+, C.L. Chuang, C.C. Wang and G.S. Shieh* (2010), "Inferring genetic Interactions via a nonlinear model and an optimization alogorithm", BMC Systems Biology. v4, 4:16. (SCI) pdf

�.  C.L. Chunag+, J.H. Wu+, C.S. Cheng and G.S. Shieh* (2010), ''WebPARE: Web-computing for inferring genetic/transcriptional interaction'', Bioinformatics, 26(4), pp. 582-584. (SCI) pdf

�.  C.L. Chuang, K. Hung, C.M. Chen* and G.S. Shieh* (2009) "Uncovering transcriptional interactions via an adaptive fuzzy logic approach", BMC Bioinformatics. v10, pp. 400-(SCI) pdf

�.  S. Kato*, K. Shimizu, and G.S. Shieh (2008) "A Circular-Circular Regression Model", Statistica Sinica, v18, pp. 633-645. (SCI) pdf

�.  C. L. Chuang, C. H. Jen, C. M. Chen and G.S. Shieh* (2008), "A Pattern Recognition Approach to Infer time-lagged Genetic Interactions", Bioinformatics, v24(9), pp. 1183-1190. (SCI) pdf

�.  G.S. Shieh*,+, C.M. Chen+, C.Y. Yu, J. Hwang, W. F. Wang and Yi-Chen Lo (2008), "Inferring transcriptional compensation interactions in yeast via stepwise structure equation modeling," BMC Bioinformatics, v9, pp. 134-143. (SCI) pdf

�.  Invited paper G.S. Shieh* and C.Y. Guo (2008), "Visualization for Genetic Networks Reconstruction," Handbooks of Computational Statistics, vol. III, pp.793-811. pdf

�.  C. L. Chuang, C. M. Chen, G.S. Shieh and J. A. Jiang (2007) "GeneCFE-ANFIS: A Neuro-Fuzzy Inference System to Infer Gene-Gene Interactions Based on Recognition of Microarray Gene Expression Patterns," Biomedical Engineering: Applications, Basis and Communications, v19(2), pp. 71-78. (EI)

�.  G.S. Shieh*, T.H. Fan and H.P. Chu (2007), "A Bayesian Approach to Assessing Differential Expressions in Microarray Data," J. Stat. Comp. Simu, v78, pp.178-191. DOI: 10.1080/10629360600954588 (SCI) pdf

�.  C. L. Chuang, C. M. Chen and G.S. Shieh, (2006) "A Hybrid Algorithm to Infer Genetic Network," Lecture Notes in Computer Science, Vol. 4233, pp. 1079-1089. (SCI / EI)pdf

�.  H.C. Ho and G.S. Shieh* (2006) "Two-stage U-statistics for Hypothesis Testing", Scandinavian. J. of Statistics, v33, pp. 861-873. (SCI) pdf

�.  G.S. Shieh*, Y.C. Jiang and Y.S. Shih (2006). "Comparison of Support Vector Machines to Other Classifiers Using Gene Expression Data," Communiaction in Statistics ---Simulation and computing, v35, pp.241-256. (SCI) pdf

�.  G.S. Shieh* and R.A. Johnson (2005). "Inference Based on A Bivariate Distribution with Von-Mises Marginals".Ann. Inst. Stat. Math., 57, pp. 789-802. (SCI) pdf

�.  G.S. Shieh*, C.H. Bai and C. Lee (2004). "Indentify Breast Cancer Subtypes by Gene expression Profiles", J. Data Science, v2, pp. 165-175. pdf

�.  R.A. Johnson* and G.S. Shieh* (2002). "On Tests of Independence for Spherical Data-Invariance and Centering", Statist. and Probab. Letters, v57, pp. 327-335. Project Number: NSC-88-2118-M-001-011. (SCI) pdf

�.  G.S. Shieh*, Z.D. Bai and W.Y. Tsai (2000). "Rank Tests for Independence with A Weighted Contamination Alternative", Statistica Sinica, v10, pp. 577-593. Project Number: NSC-86-2115-M-001-020. (SCI) pdf

�.  G.S. Shieh* (1998). "A Weighted Kendall's tau statistic", Statist. and Probab. Letters, v39, pp. 17-24. Project Number: NSC-86-2115-M-001-020. (SCI) pdf

�.  G.S. Shieh* (1997). "Weighted Degenerate U- and V-statistics with Estimated Parameters", Statistica Sinica, v7, pp. 1021-1038. Project Number: NSC-84-2121-M-001-032. (SCI) pdf

�.  G.S. Shieh* (1997). "Refined Composite Sampling for Acute Toxicity Standard", Environmetrics, v8, pp. 121-132. Project Number: NSC-84-2121-M-001-032. (SCI). pdf

�.  G.S. Shieh*, R.A. Johnson and E.W. Frees (1994). "Testing for Independence of Bivariate circular Data and Weighted Degenerate U-statistics " Statistica Sinica, v4, pp. 729-747.(SCI) pdf

�.  G.S. Shieh* (1994). "Infinite Order V-statistics", Statist. and Probab. Letters, v20, pp. 75-80. (SCI) pdf

*: corresponding author
+: contributed equally

Books

�.  G.S. Shieh* and C.Y. Guo (2008). "Visualization for Genetic Networks Reconstruction", Handbooks of Computational Statistics, vol. III, pp.793-811.

�.  G.S. Shieh and S. Kotz (2005). "Correlation Coefficients, Weighted", Encyclopedia of Statistical Sciences, 2nd Edit. Wiley, New York.

�.  G.S. Shieh (2005). "U- and V-statistics", Encyclopedia of Statistical Sciences, 2nd Edit. Wiley, New York.

�.  G.S. Shieh (1999). "U-statistics and V-statistics (Updata)", Encyclopedia of Statistical Sciences (update volume 3), pp.765-771.

Proceedings Paper

�.  C.M. Chen+, Chi Lee+, C.L. Chuang, C.C. Wang and G. S. Shieh, (2009), "A Nonlinear Model and an Optimization algorithm to Infer Genetic Interactions", Proceedings of the 2nd International Conference on Biomedical Engr. and Informatics, Tianjin, Chain.

�.  C.-L. Chuang, C.-M. Chen, G. S. Shieh and J.-A. Jiang, (2008)"A Fuzzy Logic Approach to Infer Transcriptional Regulatory Network in Saccharomyces cerevisiae using Promoter Site Prediction and Gene Expression Pattern Recognition," in Proceedings of the 2008 IEEE Congress on Evolutionary Computation, Hong Kong, June 1-6, 2008. (EI)

�.  C. L. Chuang, C. M. Chen, G.S. Shieh and J. A. Jiang, (2007) "A Neuro-Fuzzy Inference System to Infer Gene-Gene Interactions Based on Recognition of Microarray Gene Expression Patterns", in Proceedings of the 2007 IEEE Congress on Evolutionary Computation, Singapore, Sept. 25-28. (EI)

�.  C.Y. Yu, C.M. Chen, J. Huang and G.S. Shieh* (2005). "Using Covariance Structure Modeling to Reconstruct Genetic Networks", pp. 1-4, Proceedings of ISI 2005 Conference, Sydney, Australia.

�.  G.S. Shieh* (2004). "Reconstructing Gene Networks by a Data-driven Response Surface", pp. 18-31, The Cherry Bud Workshop, Yokohama, Japan.

�.  G.S. Shieh*, Y.C. Jiang, Y.C. Hung and T.F. Wang (2004), "A Regression Approach to Reconstruct Gene Networks", pp. 357-370, Proceedings of Taipei Symposium in Statistical Genomics, Taipei, Taiwan.

�.  G.S. Shieh (2004). "Reconstructing Gene Networks by a Data-driven Response Surface", pp. 18-31, The Cherry Bud Workshop, Yokohama, Japan. 

�.  Y.C. Liu, F.C. Hsieh, J.N. Chen, G. S. Shieh* and C. M. Chen (2002). "Mining Characteristic Genes That Determine the Vascularity Index of A Tumor Based on cDNA Microarrays", best graduate poster award at Annual Conference of Taiwan Biomedical Engineering Conference.

�.  G.S. Shieh* (1995). "Measuring Top-down Correlation", Proceedings of the 4th Southern Statistics Conference. pp. 37-42.

Manuscript

�.  "H2B ubiquitylation is part of chromatin architecture that marks exon-intron structure," G. S. Shieh et al. (2011) , submitted.

  • "Genes And Networks Critical for Hepatocellular Carcinogenesis in Mouse Revealed by Genomewide Gene Profiling," Ting-Feng Tsai, Grace S. Shieh, Pei-Ting Lin, Yu-I Lin, Chao-Chin Li, Shih-Feng Tsai and Chiou-Hwa Yuh* (2010), under revision.

�.  "Inferring Genetic Interactions via A Data-driven Second Order Model," C. R. Jiang, Y.C. Hung, C.M. Chen and G.S. Shieh* (2009), in preparation.

Technical Reports

�.  Grace S. Shieh*, Shurong Zheng, Richard A. Johnson, Yi-Feng Chang, Kunio Shimizu, Chia-Chang Wang and Sen-Lin Tang (2011)" Modeling and Comparing the Organization of Circular Genomes", Technical Report 11-02, Institute of Statistical Science, Academia Sinica, Taiwan.

�.  C.M. Chen+, Chih Lee+, C.L. Chuang, C.C. Wang and G.S. Shieh*(2009)" Inferring genetic networks via a nonlinear model and an optimization algorithm", Technical Report 09-06, Institute of Statistical Science, Academia Sinica, Taiwan.

�.  C.L Chuang, C.M. Chen and G.S. Shieh*(2009)"Discovering transcriptional inter-actions via a Fuzzy-logic approach", Technical Report 09-05, Institute of Statistical Science, Academia Sinica, Taiwan.

�.  G.S. Shieh*, S.R. Zheng, K. Shimizu (2006) "A Bivariate Generalized von Mises Distribution with Applications to Circular Genomes," Technical Report 06-06, Institute of Statistical Science, Academia Sinica, Taiwan.

�.  G.S. Shieh*, C.M. Chen, C.Y. Yu, J. Hwang and Weio-Fuh Wang (2006), " A stepwise Structure Equation Modeling Algorithm to Reconstruct Gene Networks," Technical Report 05-04, Institute of Statistical Science, Academia Sinica, Taiwan. Revised for Bioinformatics.

�.  C.L. Chuang, C.M. Chen and G.S. Shieh* (2005), "A Pattern Recognition Approach to Infer Genetic Networks," Technical Report 05-05, Institute of Statistical Science, Academia Sinica, Taiwan.

�.  C.M. Chen, C.F. Chang, C. Lee and G.S. Shieh* (2004)," Evaluating Genetic Networks Reconstruction by Simulated Microarray Data," Technical Report 04-02, Institute of Statistical Science, Academia Sinica, Taiwan.

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Institute of Statistical Science, Academia Sinica, 128, Academia Rd. Sec. 2, Taipei 115, Taiwan