2001-2005      Ph.D., Bioinformatics, Affiliated with Department of Genetics, North Carolina State University, USA

1996-1998      M.S., Statistics, National Tsing Hua University, Taiwan

1991-1995      B.S., Mathematics, National Taiwan University, Taiwan

Wen-Ping Hsieh  謝文萍



Tanbin Rahman, Hsin-En Huang, An-Shun Tai, Wen-Ping Hsieh, George Tseng* (2021) A sparse negative binomial classifier with covariate adjustment for RNA-seq data. Accepted by Annals of Applied Statistics.


An-Shun Tai, George C. Tseng, and Wen-Ping Hsieh* (2021). BayICE: A Bayesian hierarchical model for semi-reference-based deconvolution of bulk transcriptomic data. Annals of Applied Statistics. Vol. 15, No. 1, 391-411.


Wen-Ling Kuo, Lin-Lu Tseng, Che-Chang Chang, Chih-Jung Chen, Mei-Ling Cheng, Hsin-Hung Cheng, Meng-Jen Wu, Yu-Lun Chen, Ruei-Ting Chang, Hsiang-Yu Tang, Yong-Chen Hsu, Wen-Jye Lin, Cheng-Yuan Kao, Wen-Ping Hsieh, Hsing-Jien Kung, and Wen-Ching Wang* (2021). "Prognostic Significance of O-GlcNAc and PKM2 in Hormone Receptor-Positive and HER2-Nonenriched Breast Cancer" Diagnostics 11, no. 8: 1460.


Chih-Yung Chiu, Hsin-Cheng Chou, Lun-Ching Chang, Wen-Lang Fan, Michael Cong Vinh Dinh, Yu-Lun Kuo, Wen-Hung Chung, Hsin-Chih Lai, Wen-Ping Hsieh, Shih-Chi Su* (2020) Integration of metagenomics-metabolomics reveals specific signatures and functions of airway microbiota in mite-sensitized childhood asthma. Allergy, 75(11). doi: 10.1111/all.14438.


I-Wen Wu, Sheng-Siang Gao, Hsin-Cheng Chou, Huang-Yu Yang, Lun-Ching Chang, Yu-Lun Kuo, Michael Cong Vinh Dinh, Wen-Hung Chung, Chi-Wei Yang, Hsin-Chih Lai, Wen-Ping Hsieh, Shih-Chi Su*. Integrative metagenomic and metabolomic analyses reveal severity-specific signatures of gut microbiota in chronic kidney disease. Theranostics. 2020;10(12):5398-5411.


I-Wen Wu, Chan-Yu Lin, Lun-Ching Chang, Chin-Chan Lee, Chih-Yung Chiu, Heng-Jung Hsu, Chiao-Yin Sun, Yuen-Chan Chen, Yu-Lun Kuo, Chi-Wei Yang, Sheng-Siang Gao, Wen-Ping Hsieh, Wen-Hung Chung, Hsin-Chih Lai, Shih-Chi Su*. Gut Microbiota as Diagnostic Tools for Mirroring Disease Progression and Circulating Nephrotoxin Levels in Chronic Kidney Disease: Discovery and Validation Study. Int J Biol Sci. 2020 Jan 1;16(3):420-434.


Ki-Hok Liao, Wing-Kai Hon, Chuan-Yi Tang, Wen-Ping Hsieh*. (2019) MetaSMC: A Coalescent-based Shotgun Sequence Simulator for Evolving Microbial Populations. Bioinformatics.35(10):1677-1685.


An-Shun Tai, Chien-Hua Peng*, Shih-Chi Peng, Wen-Ping Hsieh* (2018). Decomposing the subclonal structure of tumors with two-way mixture models on copy number aberrations. PLoS ONE 13(12): e0206579.


Chien-Hua Peng, Chun-Ta Liao, Ka-Pou Ng, An-Shun Tai, Shih-Chi Peng,  Jen-Pao Yeh, Shu-Jen Chen, Kuo-Chien Tsao, Tzu-Chen Yen *, and Wen-Ping Hsieh*. (2015) Somatic copy number alterations detected by ultra-deep targeted sequencing predict prognosis in oral cavity squamous cell carcinoma. Oncotarget 2015 Aug 14;6(23):19891-906.


Shih-Chi Peng, Chun-Ta Liao, Chien-Hua Peng, Ann-Joy Cheng, Shu-Jen Chen, Chung-Guei Huang, Wen-Ping Hsieh*, Tzu-Chen Yen*. (2014) MicroRNAs miR-218, miR-125b, and let-7g Predict Prognosis in Patients with Oral Cavity Squamous Cell Carcinoma. PLoS ONE, 9(7): e102403. doi: 10.1371/journal.pone.0102403

Yen-Jen Lin, Yu-Tin Chen, Shu-Ni Hsu, Chien-Hua Peng, Chuan-Yi Tang, Tzu-Chen Yen, Wen-Ping Hsieh* (2014) HaplotypeCN: Copy number haplotype inference with Hidden Markov Model and localized haplotype cluster. PLoS ONE 9(5): e96841. doi:10.1371/journal.pone.0096841

Pei-Wen Tsai, Yu-Ting Chen, Cheng-Yao Yang, Hsueh-Fen Chen, Te-Sheng Tan, Tzung-Wei Lin, Wen-Ping Hsieh*, Chung-Yu Lan* (2014) The role of Mss11 in Candida albicans biofilm formation. Molecular Genetics and Genomics 289(5):807-19.

Yu-Chao Wang, I-Chun Tsai, Che Lin, Wen-Ping Hsieh, Chung-Yu Lan, Yung-Jen Chuang and Bor-Sen Chen. (2014) "Essential Functional Modules for Pathogenic and Defensive Mechanisms in Candida albicans Infections," BioMed Research International, vol. 2014, Article ID 136130, 15 pages, 2014. doi:10.1155/2014/136130.

Lai CC, Yeh YH, Hsieh WP, Kuo CT, Wang WC, et al. (2013) Whole-Exome Sequencing to Identify a Novel LMNA Gene Mutation Associated with Inherited Cardiac Conduction Disease. PLoS ONE 8(12): e83322. doi:10.1371/journal.pone.0083322

Peng CH; Jiang YZ; Tai AS; Liu CB; Peng SC; Liao CT; Yen TC; Hsieh WP*. (2013) Causal inference of gene regulation with subnetwork assembly from genetical genomics data. Nucleic Acids Research; doi: 10.1093/nar/gkt1277.

Wang YC, Lin C, Chuang MT, Hsieh WP, Lan CY, Chuang YJ, Chen BS. (2013) Interspecies protein-protein interaction network construction for characterization of host-pathogen interactions: a Candida albicans-zebrafish interaction study. BMC Syst Biol. 2013 Aug 16;7:79. doi: 10.1186/1752-0509-7-79.

Chen YY, Chao CC, Liu FC, Hsu PC, Chen HF, Peng SC, Chuang YJ, Lan CY, Hsieh WP, Wong DS. (2013) Dynamic transcript profiling of Candida albicans infection in zebrafish: a pathogen-host interaction study. PLoS One. 2013 Sep 03; 10.1371/ journal.pone.0072483

Lin YJ, Chang CT, Tang CY, and Hsieh WP*. (2013) Simpute: An Efficient Solution for Dense Genotypic Data. BioMed Research International, Volume 2013, Article ID 813912


Chen YT, Lin CY, Tsai PW, Yang CY, Hsieh WP, Lan CY. (2011) Rhb1 regulates the expression of secreted aspartic protease 2 through the TOR signaling pathway in Candida  albicans. Eukaryotic Cell, doi: 10.1128/​EC.05200-11


Peng CH, Liao CT, Peng SC, Chen YJ, Cheng AJ, Juang JL, Tsai CY, Chen TC, Chuang YJ, Tang CY, Hsieh WP*, Yen TC* (2011) A Novel Molecular Signature Identified by Systems Genetics Approach Predicts Prognosis in Oral Squamous Cell Carcinoma. PLoS One, 6(8): e23452. doi:10.1371/journal.pone.0023452

Hsieh WP*, Chu TM, Lin YM, Wolfinger RD. (2011) Kernel density weighted loess normalization improves the performance of detection within asymmetrical data. BMC Bioinformatics, 12:222


Hsu JT, Peng CH, Hsieh WP, Lan CY, Tang CY. (2011) A novel method to identify cooperative functional modules: study of module coordination in the Saccharomyces cerevisiae cell cycle. BMC Bioinformatics, 12:281.


Chang PC, Fitzgerald LD, Hsia DA, Izumiya Y, Wu CY, Hsieh WP, Lin SF, Campbell M, Lam KS, Luciw PA, Tepper CG, Kung HJ. (2011) Histone demethylase JMJD2A regulates KSHV replication and is targeted by a viral transcriptional factor. Journal of Virology, doi:10.1128/JVI.02485-10


Wang YC, Lan CY, Hsieh WP, Murillo LA, Agabian N, Chen BS. (2010) Global screening of potential Candida albicans biofilm-related transcription factors via network comparison. BMC Bioinformatics, 11:53


Hsieh WP*, Chu TM, and Wolfinger RD. (2007) Comparison of statistical performance of univariate and bivariate mixed models for Affymetrix probe level data. Journal of Statistical Computation and Simulation. 77(3) 251-264.


Passador-Gurgel G, Hsieh WP, Hunt P, Deighton N, Gibson G. (2007) Quantitative Trait Transcripts for Nicotine Resistance in Drosophila melanogaster. Nature genetics, 39(2):264-8.


Hsieh WP, Passador-Gurgel G, Stone EA, Gibson G. (2007)  Mixture modeling of transcript abundance classes in natural populations. Genome Biology, 8(6):R98


Tsai S, Mir B, Martin AC, Estrada JL, Bischoff SR, Hsieh WP, Cassady JP, Freking BA, Nonneman DJ, Rohrer GA, Piedrahita JA. (2006) Detection of transcriptional difference of porcine imprinted genes using different microarray platforms. BMC Genomics, 7:328.


Hsieh WP, Chu TM, Wolfinger RD, and Gibson G. (2003) Mixed model reanalysis of primate data suggests tissue and species biases in oligonucleotide-based gene expression profiles. Genetics, 165: 747-757.

Last update: Sep. 29, 2021


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Research Interest


Bioinformatics, Systems Biology

Associate Professor

Institute of Statistics

National Tsing Hua University