Journal

  1. Chen BS*, Wang YC, Wu WS, Li WH, “A new measure of robustness of biochemical networks” Bioinformatics, 21(11):2698-2705, 2005.
  2. Chen BS*, Wang YC, “On the attenuation and amplification of molecular noise in genetic regulatory networks” BMC Bioinformatics, 7:52, 2006.
  3. Chang YH†, Wang YC†, Chen BS*, “Identification of transcription factor cooperativity via stochastic system model” Bioinformatics, 22(18):2276-2282, 2006. †co-first author
  4. Chang YH, Wang YC, Chen BS*, “Nonlinear dynamic trans/cis regulatory circuit for gene transcription via microarray data” Gene Regulation and Systems Biology, 1:151-166, 2007.
  5. Chen BS*, Wu WS, Wang YC, Li WH, “On the robust circuit design schemes of biochemical networks: steady-state approach” IEEE Transactions on Biomedical Circuits and Systems, 1(2):91-104, 2007.
  6. Chen BS*, Chang YT, Wang YC, “Robust H∞-stabilization design in gene networks under stochastic molecular noises: fuzzy-interpolation approach” IEEE Transactions on System, Man and Cybernetics Part B: Cybernetics, 38(1):25-42, 2008.
  7. Wang YC, Lan CY, Hsieh WP, Murillo L, Agabian N, Chen BS*, “Global screening of potential Candida albicans biofilm-related transcription factors via network comparison” BMC Bioinformatics, 11:53, 2010.
  8. Wang YC, Chen BS*, “Integrated cellular network of transcription regulations and protein-protein interactions” BMC Systems Biology, 4:20, 2010.
  9. Yang SK†, Wang YC†, Chao CC, Chuang YJ, Lan CY, Chen BS*, “Dynamic cross-talk analysis among TNF-R, TLR-4 and IL-1R signalings in TNFα-induced inflammatory responses” BMC Medical Genomics, 3:19, 2010. †co-first author
  10. Wang YC, Chen BS*, “A network-based biomarker approach for molecular investigation and diagnosis of lung cancer” BMC Medical Genomics, 4:2, 2011.
  11. Chen BS*, Chang CH, Wang YC, Wu CH, Lee HC, “Robust model matching design methodology for a stochastic synthetic gene network” Mathematical Biosciences, 230(1):23-36, 2011.
  12. Wang YC, Huang SH, Lan CY, Chen BS*, “Prediction of phenotype-associated genes via a cellular network approach: a Candida albicans infection case study” PLoS ONE, 7(4):e35339, 2012.
  13. Wang YC, Lin C, Chuang MT, Hsieh WP, Lan CY, Chuang YJ, Chen BS*, “Interspecies protein-protein interaction network construction for characterization of host-pathogen interactions: a Candida albicans-zebrafish interaction study” BMC Systems Biology, 7:79, 2013.
  14. Yang TH, Wang CC, Wang YC, Wu WS*, “YTRP: a repository for yeast transcriptional regulatory pathways” Database: The Journal of Biological Databases and Curation, 2014:bau014, 2014.
  15. Wang YC†*, Tsai IC†, Lin C, Hsieh WP, Lan CY, Chuang YJ, Chen BS*, “Essential functional modules for pathogenic and defensive mechanisms in Candida albicans infections” BioMed Research International, 2014:136130, 2014. †co-first author
  16. Lin C*, Lin CN, Wang YC, Liu FY, Chuang YJ, Lan CY, Hsieh WP, Chen BS, “The role of TGF-β signaling and apoptosis in innate and adaptive immunity in zebrafish: a systems biology approach” BMC Systems Biology, 8:116, 2014.
  17. Lin C*, Lin CN, Wang YC, Liu FY, Chien YW, Chuang YJ, Lan CY, Hsieh WP, Chen BS, “Robustness analysis on interspecies interaction network for iron and glucose competition between Candida albicans and zebrafish during infection” BMC Systems Biology, 8(Suppl 5):S6, 2014.
  18. Hu CW, Hsu CL, Wang YC, Ishihama Y, Ku WC, Huang HC*, Juan HF*, “Temporal phosphoproteome dynamics induced by an ATP synthase inhibitor citreoviridin” Molecular & Cellular Proteomics, 14(12):3284-3298, 2015.
  19. Yeh YC, Lei HJ, Chen MH, Ho HL, Chiu LY, Li CP, Wang YC*, “C-reactive protein (CRP) is a promising diagnostic immunohistochemical marker for intrahepatic cholangiocarcinoma and is associated with better prognosis” American Journal of Surgical Pathology, 41(12):1630-1641, 2017. link
  20. Lyu GY, Yeh YH, Yeh YC*, Wang YC*, “Mutation load estimation model as a predictor of the response to cancer immunotherapy” npj Genomic Medicine, 3:12, 2018. link
  21. Yeh YC, Ho HL, Wu YC, Pan CC, Wang YC*, Chou TY*, “AKT1 internal tandem duplications and point mutations are the genetic hallmarks of sclerosing pneumocytoma” Modern Pathology, 33(3):391-403, 2020. link
  22. Tan KT, Yeh CN, Chang YC, Cheng JH, Fang WL, Yeh YC, Wang YC, Hsu DS, Wu CE, Lai JI, Chang PM, Chen MH, Lu ML, Chen SJ, Chao Y, Hsiao M, Chen MH*, “PRKDC: new biomarker and drug target for checkpoint blockade immunotherapy” Journal for ImmunoTherapy of Cancer, 8:e000485, 2020. link
  23. Pan CC*, Yeh YC, Wang YC, Chang YH, “Differential expression analysis of clear cell renal cell carcinomas in The Cancer Genome Atlas distinguishes an aggressive subset enriched with chromosomes 7 and 12 gains” Histopathology, 76(7):950-958, 2020. link
  24. Pan YR†, Wu CE†, Wang YC†, Yeh YC, Lu ML, Hung YP, Chao Y, Yeh DW, Lin CH, Hsieh JCH, Chen MH*, Yeh CN*, “Establishment of a novel gene panel as a biomarker of immune checkpoint inhibitor response” Clinical & Translational Immunology, 9(7):e1145, 2020. †co-first author link
  25. Wu CE, Yeh DW, Pan YR, Huang WK, Chen MH, Chang JW, Chen JS, Wang YC*, Yeh CN*, “Chromosomal instability may not be a predictor for immune checkpoint inhibitors from comprehensive bioinformatics analysis” Life (Basel), 10(11):276, 2020. link
  26. Huang YF, Chang CH, Chen PJ, Lin IH, Tsai YA, Chen CF, Wang YC, Huang WY, Tsai MS*, Chen ML*, “Prenatal bisphenol A exposure, DNA methylation, and low birth weight: a pilot study in Taiwan” International Journal of Environmental Research and Public Health, 18(11):6144, 2021. link
  27. Chiu TY, Lin RW, Huang CJ, Yeh DW, Wang YC*, “DNA damage repair gene set as a potential biomarker for stratifying patients with high tumor mutational burden” Biology (Basel), 10(6):528, 2021. link
  28. Huang CJ, Wang LH, Wang YC*, “Identification of therapeutic targets for the selective killing of HBV-positive hepatocytes” Journal of Personalized Medicine, 11(7):649, 2021. link
  29. Yeh YC, Ho HL, Lin CI, Chou TY, Wang YC*, “Whole-exome sequencing of Epstein–Barr virus-associated pulmonary carcinoma with low lymphocytic infiltration reveals molecular features similar to those of classic pulmonary lymphoepithelioma-like carcinoma: Evidence to support grouping together as one disease entity” American Journal of Surgical Pathology, 45(11):1476-1486, 2021. link
  30. Lin YY†, Wang YC†, Yeh DW, Hung CY, Yeh YC, Ho HL, Mon HC, Chen MY, Wu YC, Chou TY*, “Gene expression profile in primary tumor is associated with brain-tropism of metastasis from lung adenocarcinoma” International Journal of Molecular Sciences, 22(24):13374, 2021. †co-first author link
  31. Yu HY, Li CP, Huang YH, Hsu SJ, Wang YP, Hsieh YC, Fang WL, Huang KH, Li AF, Lee RC, Lee KL, Wu YH, Lai IC, Yang WC, Hung YP, Wang YC, Chen SH, Chen MH*, Chao Y*, “Microsatellite instability, Epstein–Barr virus, and programmed cell death ligand 1 as predictive markers for immunotherapy in gastric cancer” Cancers, 14(1):218, 2022. link
  32. Pan CC*, Tseng CE, Kuroda N, Yano M, Yasuda M, Nagashima Y, Yeh YC, Wang YC, Chang YH, Epstein JI, “Molecular characterization of metanephric adenoma, epithelial Wilms tumor and overlap lesions: An integrated whole exome and transcriptome sequencing analysis” Applied Immunohistochemistry & Molecular Morphology, 30(4):257-263, 2022. link
  33. Sanmarco LM†, Chao CC†, Wang YC†, Kenison JE†, Li Z, Rone JM, Rejano-Gordillo CM, Polonio CM, Gutierrez-Vazquez C, Piester G, Plasencia A, Li L, Giovannoni F, Lee HG, Faust Akl C, Wheeler MA, Mascanfroni I, Jaronen M, Alsuwailm M, Hewson P, Yeste A, Andersen BM, Franks DG, Huang CJ, Ekwudo M, Tjon EC, Rothhammer V, Takenaka M, de Lima KA, Linnerbauer M, Guo L, Covacu R, Queva H, Fonseca-Castro PH, Bladi MA, Cox LM, Hodgetts KJ, Hahn ME, Mildner A, Korzenik J, Hauser R, Snapper SB, Quintana FJ*, “Identification of environmental factors that promote intestinal inflammation” Nature, 611(7937):801-809, 2022. †co-first author link
  34. Chen TH, Chen MH, Hung YP, Chiang NJ, Huang KH, Lin YH, Lin RW, Chao Y, Li AF, Yu HY, Huang HE, Yeh YC, Wang YC*, Fang WL*, “Elevated PD-L1 expression and microsatellite instability in elderly patients with gastric cancer” Journal of Immunotherapy, 46(3):111-119, 2023. link
  35. Chang JW, Huang CJ, Huang WK, Wang YC, Hsieh JJ, Chang YY, Huang YL, Wu CL, Wang YH, Chen SJ, Tan KT, Chen CP, Wu CE*, “Genomic and tumour microenvironmental biomarkers of immune checkpoint inhibitor response in advanced Taiwanese melanoma” Clinical & Translational Immunology, 12(8):e1465, 2023.  link
  36. Yeh YC*, Chu PY, Lin SY, Wang SY, Ho HL, Wang YC*, “Comprehensive genomic and transcriptomic analysis of sclerosing pneumocytoma” Modern Pathology, 37(1):100354, 2024.  link
  37. Jeng KS, Cheng PY, Lin YH, Liu PC, Tseng PH, Wang YC, Chang CF, Leu CM*, “Aldo-keto reductase family member C3 (AKR1C3) promotes hepatocellular carcinoma cell growth by producing prostaglandin F2α” Oncology Research, 32(1): 163-174, 2024. link
  38. Chen PA, Chang PC, Yeh WW, Hu TY, Hong YC, Wang YC, Huang WJ, Lin TP*, “The lncRNA TPT1-AS1 promotes the survival of neuroendocrine prostate cancer cells by facilitating autophagy” American Journal of Cancer Research, 14(5): 2103-2123, 2024. link
  39. Wu CH, Lai CL, Hsu YC, Hsu CY, Wang YC, Lin HC*, “Pre-treatment pan-immune-inflammation value as a prognostic marker of pazopanib in soft tissue sarcoma” Therapeutic Advances in Medical Oncology, 16:17588359241292255, 2024. link

Conference / Poster

  1. Wang YC, Chen BS, “Robust PI regulation control in metabolic pathway” Cold Spring Harbor Laboratory Meeting – Engineering Principles in Biological Systems, New York, USA, December 3-6, 2006.
  2. Wang YC, Chen BS, “Molecular investigation and diagnosis of lung cancer via the network-based biomarker” The 8th Asian Control Conference, Kaohsiung, Taiwan, May 15-18, 2011.
  3. Wang YC, Tsai IC, Chao CC, Lin C, Hsieh WP, Lan CY, Chuang YJ, Chen BS, “Differential network analysis reveals essential functional modules in Candida albicans infections” The 13th International Conference on Systems Biology (ICSB 2012), Toronto, Canada, August 19-23, 2012.
  4. Wu CH, Lin YH, Hsu CL, Wang YC, Lin WC, Juan HF, Huang HC, “Identification of lncRNA-regulated protein-protein interaction networks and their functions” The 19th Biophysics Conference, Tainan, Taiwan, May 7-10, 2014.
  5. Hsu MJ, Wang YC, Juan HF, Huang HC, “Characterization and stratification of lncRNA and ceRNA modulation networks” The 19th Biophysics Conference, Tainan, Taiwan, May 7-10, 2014.
  6. Wang YC, Lin C, Hsieh WP, Lan CY, Chuang YJ, Chen BS, “Integrative network analysis of Candida albicans-zebrafish interaction” The 22nd International Conference on Intelligent Systems for Molecular Biology (ISMB 2014), Boston, USA, July 13-15, 2014.
  7. Hu CW, Hsu CL, Wang YC, Ishihama Y, Ku WC, Huang HC, Juan HF, “Temporal phosphoproteome dynamics reveal response pathways of ectopic ATP synthase blockade” The 73rd Annual Meeting of the Japanese Cancer Association, Yokohama, Japan, September 25-27, 2014.
  8. Yu WH, Wang YC, Juan HF, Huang HC, “Network-based identification and stratification of lncRNA modulation network with ceRNA hypothesis” TPS2014 Translational and Systems Biology Symposium, Taipei, Taiwan, November 11-12, 2014.
  9. Lin C, Lin CN, Wang YC, Liu FY, Chien YW, Chuang YJ, Lan CY, Hsieh WP, Chen BS, “Robustness analysis on interspecies interaction network for iron and glucose competition between Candida albicans and zebrafish during infection” GIW / ISCB-Asia 2014, Tokyo, Japan, December 15-17, 2014.
  10. Yang PJ, Chen BS, Wang YC, “Construction of characterized synthetic libraries for gene circuit design with design specifications” 2015 The 30th Joint Annual Conference of Biomedical Science, Taipei, Taiwan, March 21-22, 2015.
  11. Lu HY, Sun CT, Chuang YJ, Lan CY, Chen BS, Wang YC, “Systems biology analysis of Candida albicans facing innate and adaptive immunity” 2015 The 30th Joint Annual Conference of Biomedical Science, Taipei, Taiwan, March 21-22, 2015.
  12. Chiu LY, Yeh YC, Wang YC, “Identification of potential diagnostic biomarkers and carcinogenesis-associated gene modules for cholangiocarcinoma based on integrative analysis of gene expression data” The 21st Biophysics Conference, Hsinchu, Taiwan, May 19-21, 2016.
  13. Chen TY, Wang YC, “Investigating the functions of unannotated genes using LINCS L1000 big data” The 21st Biophysics Conference, Hsinchu, Taiwan, May 19-21, 2016.
  14. Lyu GY, Yeh YC, Wang YC, “Construction of mutation burden prediction model for predicting efficacy of cancer immunotherapy” The Fifteenth Asia Pacific Bioinformatics Conference (APBC2017), Shenzhen, China, January 16-18, 2017.
  15. Wu CT, Wang YC, “Identification of potential disease genes for lung adenocarcinoma using integrated omics data analysis” The 22nd Biophysics Conference, Kaohsiung, Taiwan, May 17-20, 2017.
  16. Wang YC, Lyu GY, Yeh YC, “Identification of genomic predictors for treatment response to cancer immunotherapy” The 25th International Conference on Intelligent Systems for Molecular Biology (ISMB 2017), Prague, Czech, July 21-25, 2017.
  17. Wang YC, Lyu GY, Yeh YC, “Mutation load estimation model as a predictor for cancer immunotherapy treatment response” The 76th Annual Meeting of the Japanese Cancer Association (JCA 2017), Yokohama, Japan, September 28-30, 2017.(Travel Grant Award)
  18. Yeh DW, Wang YC, “Identification of high mutation load associated genes and pathways across different cancers” The 23rd Biophysics Conference, Taichung, Taiwan, May 23-25, 2018.
  19. Huang CJ, Wang YC, “Identification of the therapeutic targets for selective killing of HBV-positive hepatocytes” The 17th Asia Pacific Bioinformatics Conference (APBC2019), Wuhan, China, January 14-16, 2019.
  20. Chiu TY, Wang YC, “Investigation of the association between the mutational landscape of DNA damage repair genes with high tumor mutational burden in different cancers” 2019 The 34th Joint Annual Conference of Biomedical Science, Taipei, Taiwan, March 23-24, 2019.
  21. Chang YC, Wang YC, “Investigation of the influencing factors of microsatellite instability (MSI) status across different cancer types” 2019 The 34th Joint Annual Conference of Biomedical Science, Taipei, Taiwan, March 23-24, 2019.
  22. Huang WN, Wang YC, “Classification of cancer subtypes using the cell populations of tumor infiltrating lymphocytes” 2019 The 34th Joint Annual Conference of Biomedical Science, Taipei, Taiwan, March 23-24, 2019.
  23. Yeh DW, Chiu TY, Chang YC, Yeh YC, Chen MH, Wang YC, “Investigation of the association between mutational landscape of DNA repair genes and treatment response to cancer immunotherapy” The 27th International Conference on Intelligent Systems for Molecular Biology (ISMB 2019), Basel, Switzerland, July 21-25, 2019.
  24. Lin WY, Wang YC, “Exploring the association between calcium ion binding genes and tumor mutation burden” International Symposium on Evolutionary Genomics and Bioinformatics 2023 (ISEGB 2023), Hsinchu, Taiwan, June 29-30, 2023.
    * Best Poster Award
  25. Hsu YT, Yeh YC, Huang CJ, Wang YC, “Investigation of internal tandem duplication (ITD) across different cancer types” International Symposium on Evolutionary Genomics and Bioinformatics 2023 (ISEGB 2023), Hsinchu, Taiwan, June 29-30, 2023.
    * Best Poster Award
  26. Lin WY, Wang YC, “Exploring the association between calcium ion binding genes and tumor mutation burden” The 31st Annual Intelligent Systems For Molecular Biology and the 22nd Annual European Conference on Computational Biology (ISMB/ECCB 2023), Lyon, France, July 23-27, 2023.
  27. Hsu YT, Yeh YC, Huang CJ, Wang YC, “Investigation of internal tandem duplication (ITD) across different cancer types” The 31st Annual Intelligent Systems For Molecular Biology and the 22nd Annual European Conference on Computational Biology (ISMB/ECCB 2023), Lyon, France, July 23-27, 2023.
  28. Huang CJ, Yeh YC, Wang YC, “Characterization of lung adenosquamous carcinoma with genomics analysis” The 31st Annual Intelligent Systems For Molecular Biology and the 22nd Annual European Conference on Computational Biology (ISMB/ECCB 2023), Lyon, France, July 23-27, 2023.
  29. Liu GT, Wang YC, “Construction of immune hot/cold tumor classification model for gastrointestinal cancers” 2023 Multiomics and Precision Medicine Joint Conference (MOPM 2023), Taipei, Taiwan, November 11-12, 2023.
    * Best Poster Award
  30. Hii LA, Hsu YT, Yeh YC, Wang YC, “Investigation of the genomic landscape of internal tandem duplication (ITD) in tumor” 2024 SMBE Regional Meeting in Taiwan, Taipei, Taiwan, March 28-30, 2024.
  31. Lien JY, Lin SF, Wang YC, “Exploring potential methylation markers for ovarian cancer by cervical scraping samples” 2024 SMBE Regional Meeting in Taiwan, Taipei, Taiwan, March 28-30, 2024.
    * Best Poster Award
  32. Hii LA, Hsu YT, Yeh YC, Wang YC, “Investigation of the genomic landscape of internal tandem duplication (ITD) in tumors” The 32nd International Conference on Intelligent Systems for Molecular Biology (ISMB 2024), Montreal, Canada, July 12-16, 2024.
  33. Wang SC, Wang YC, “Investigation of homologous recombination deficiency (HRD) based on next-generation sequencing data” The 32nd International Conference on Intelligent Systems for Molecular Biology (ISMB 2024), Montreal, Canada, July 12-16, 2024.
  34. Lien JY, Wang YC, “Exploring potential methylation markers for ovarian cancer by cervical scraping samples” The 32nd International Conference on Intelligent Systems for Molecular Biology (ISMB 2024), Montreal, Canada, July 12-16, 2024.
  35. Chang HY, Huang CJ, Yeh YC, Wang YC, “Comparison of colon cancer genomics between Eastern and Western populations” 1st Asia & Pacific Bioinformatics Joint Conference  (APBJC 2024), Okinawa, Japan, October 22-25, 2024.
  36. Juan LH, Hii LA, Hsu YT, Yeh YC, Wang YC, “Comprehensive analysis of internal tandem duplications across various cancers” 1st Asia & Pacific Bioinformatics Joint Conference  (APBJC 2024), Okinawa, Japan, October 22-25, 2024.
  37. Juan LH, Hii LA, Hsu YT, Yeh YC, Wang YC, “Comprehensive analysis of internal tandem duplications across various cancers” 2024 Multiomics and Precision Medicine Joint Conference (MOPM 2024), Taipei, Taiwan, November 9-10, 2024.
    * Best Poster Award

Book

  1. Chen BS and Wang YC, Synthetic Gene Network: Modeling, Analysis and Robust Design Methods, CRC Press, 2014.