Chang HY, Huang CJ, Yeh YC^*, Wang YC^*

Uniform processing of diverse sequencing data: A cross-population comparison of colon cancer genomic landscapes from The Cancer Genome Atlas and a Chinese cohort

Cancer Epidemiology, Biomarkers & Prevention, 35(5):762-772

2026

Chen YJ, Chang KH, Wang YC

Elucidating immune dysregulation in neuromyelitis optica spectrum disorder through bulk and single-cell RNA-seq characterization of interferon-related gene expression

The 34th International Conference on Intelligent Systems for Molecular Biology (ISMB 2026), Washington, D.C., USA, July 12-16, 2026

Cheng KW, Wang YC

Prediction of nivolumab clinical response using tumor microenvironment-related multi-omics features across diverse cancer histologies

The 34th International Conference on Intelligent Systems for Molecular Biology (ISMB 2026), Washington, D.C., USA, July 12-16, 2026

Chang WC, Yeh YC, Wang YC

An ensemble-based multi-omics feature selection framework for cross-cancer identification of tertiary lymphoid structure signatures

The 34th International Conference on Intelligent Systems for Molecular Biology (ISMB 2026), Washington, D.C., USA, July 12-16, 2026

Chung SY^†, Yeh YC^†, Huang CJ^†, Chiang NJ, Hsu DS, Chan MH, Lu ML, Hsu TS, Hung YP, Yeh CN, Hsiao M, Chang YC^*, Wang YC^*, Chen MH^*

Comparative impact of tertiary lymphoid structures and tumor-infiltrating lymphocytes in cholangiocarcinoma

Journal for ImmunoTherapy of Cancer, 13(1):e010173

2025

Huang CJ^†, Liu GT^†, Yeh YC^†, Chung SY, Chang YC, Chiang NJ, Lu ML, Huang WN, Chen MH^*, Wang YC^*

Construction of hot tumor classification models in gastrointestinal cancers

Journal of Translational Medicine, 23(1):218

2025

Lien JY, Hii LA, Su PH, Chen LY, Wen KC, Lai HC^*, Wang YC^*

Exploring potential methylation markers for ovarian cancer from cervical scraping samples

Human Genomics, 19 (1):56

2025

Lin WY, Huang CJ, Wang YC^*

Calcium ion-binding genes can predict tumor mutation burden and immune checkpoint blockade response in a pan-cancer model

Discover Oncology, 16 (1):1341

2025

Juan LH, Hii LA, Hsu YT, Yeh YC, Wang YC

Pan-cancer profiling of internal tandem duplications reveals recurrent and cancer-specific events

29th Annual International Conference on Research in Computational Molecular Biology (RECOMB 2025), Seoul, Korea, April 26-29, 2025

Chen YY, Huang CJ, Chen TH, Wang YC

Clinical and genomic markers distinguishing recurrent and non-recurrent head and neck squamous cell carcinoma after concurrent chemoradiotherapy

29th Annual International Conference on Research in Computational Molecular Biology (RECOMB 2025), Seoul, Korea, April 26-29, 2025

Liu DY, Huang CJ, Yeh YC, Wang YC

Genomic landscape of lung adenosquamous carcinoma: A comparative analysis with lung adenocarcinoma and squamous cell carcinoma

29th Annual International Conference on Research in Computational Molecular Biology (RECOMB 2025), Seoul, Korea, April 26-29, 2025

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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)

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Chen BS and Wang YC

Synthetic Gene Network: Modeling, Analysis and Robust Design Methods

CRC Press,

2014

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

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

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

Wang YC, Chen BS^*

A network-based biomarker approach for molecular investigation and diagnosis of lung cancer

BMC Medical Genomics, 4:2

2011

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

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

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

Wang YC, Chen BS^*

Integrated cellular network of transcription regulations and protein-protein interactions

BMC Systems Biology, 4:20

2010

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

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

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

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

Chen BS^*, Wang YC

On the attenuation and amplification of molecular noise in genetic regulatory networks

BMC Bioinformatics, 7:52

2006

Chang YH^†, Wang YC^†, Chen BS^*

Identification of transcription factor cooperativity via stochastic system model

Bioinformatics, 22(18):2276-2282

2006† co-first author

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

Chen BS^*, Wang YC, Wu WS, Li WH

A new measure of robustness of biochemical networks

Bioinformatics, 21(11):2698-2705

2005