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Hsin-Chou Yang

Institute of Statistical Science, Academia Sinica
Taipei 11529, Taiwan, R.O.C.
Tel: +886-27835611 ext. 113
FAX: +886-2-27831523
E-mail: hsinchou@stat.sinica.edu.tw


Recent Research Achievements (中文, English)


Research Interests (PDF1, PDF2)



Genetic/Genomic Statistics - Identify disease susceptibility genes by using genetic marker data



Ecological Statistics - Study population abundance by using capture recapture data




1990 - 1994

B.S., Department of Statistics, National Cheng Kung University



1994 - 1996

M.S., Graduate Institute of Statistics, National Cheng Kung University



1996 - 2002

Ph.D., Institute of Statistics, National Tsing Hua University

Professional Experience 



2002.10 - 2004.06

Postdoctoral Fellow of National Science Council @ Institute of Biomedical Sciences, Academia Sinica [In military service]



2004.07 - 2006.06

Postdoctoral Fellow of Academia Sinica @ Institute of Biomedical Sciences, Academia Sinica [In military service]



2006.07 - 2011.03

2011.03 - Present

Assistant Research Fellow @ Institute of Statistical Science, Academia Sinica

Associate Research Fellow @ Institute of Statistical Science, Academia Sinica

Publications (CA Correspondence author; EC Equal contribution)


- Journal Papers 




Huggins, R. M.CA, Yang, H.-C., Chao, A. and Yip, P. S. F. (2003/05). Population size estimation using local sample coverage for open populations. Journal of Statistical Planning and Inference 113, 699-714. [SCI]




Yang, H.-C. and Huggins, R. M.CA (2003/06). The estimation of the size of an open population using local estimating equations. Statistica Sinica 13, 673-689. [SCI]




Yang, H.-C., Huggins, R. M.CA and Clark, A. (2003/06). Estimation of the size of an open population using local estimating equations II: A semi-parametric approach. Biometrics 59, 365-374. [SCI]




Lin, Y. M. J., Yang, H.-C., Lai, T. J., Fann, C. S. J. and Sun, H. S.CA (2003/10). Receptor mediated effect of serotonergic transmission in patients with bipolar affective disorder. Journal of Medical Genetics 40, 781-786. [SCI]




Yang, H.-C., Pan C.-C., Lu, R. C. Y. and Fann, C. S. J.CA (2005/01). New adjustment factors and sample size calculation in a DNA-pooling experiment with preferential amplification. Genetics 169, 399-410. [SCI]




Yang, H.-C., Chambers, L. and Huggins, R. M.CA (2005/04). A seasonal decomposition of the estimated size of a penguin population at Phillip Island, Australia. Australian Journal of Zoology 53, 111-115. [SCI]




Lo, Y.-L., Yu, J.-C., Chen, S.-T., Yang, H.-C., Fann, C. S. J., Mau, Y.-C. and Shen, C.-Y.CA (2005/06). Breast cancer risk associated with genotypic polymorphism of the mitosis-regulating gene, Aurora-A/STK15/BTAK. International Journal of Cancer 115, 276-283. [SCI]




Yang, H.-C., Chang, C.-C., Lin, C.-Y., Chen, C.-L., Lin, C.-Y. and Fann, C. S. J.CA (2005/12). A genome-wide scanning and fine mapping study of COGA data. BMC Genetics 6, S30. [SCI]




Yang, H.-C.CA and Chao, A. (2005/12). Modeling animals’ behavioral response by Markov chain models for capture-recapture experiments. Biometrics 61, 1010-1017. [SCI]




Yang, H.-C., Pan, C.-C., Lin, C.-Y. and Fann, C. S. J.CA (2006/04). PDA: Pooled DNA analyzer. BMC Bioinformatics 7, 233. [SCI]




Yang, H.-C., Lin, C.-H., Hung, S.-I. and Fann, C. S. J.CA (2006/05). A comparison of individual genotyping and pooled DNA analysis for polymorphism validation prior to large-scale genetic studies. Annals of Human Genetics 70, 350-359. [SCI]




Yang, H.-C., Lin, C.-H., Hsu, C.-L., Hung, S.-I., Wu, J.-Y., Pan, W.-H., Chen, Y.-T. and Fann, C. S. J.CA (2006/07). A comparison of major histocompatibility complex SNPs in Han Chinese residing in Taiwan and Caucasians. Journal of Biomedical Science 13, 489-498. [SCI]




Yang, H.-C., Liang, Y.-J., Huang, M.-C., Li, L.-H., Lin, C.-H., Wu, J.-Y., Chen, Y.-T. and Fann, C. S. J.CA (2006/08). A genome-wide study of preferential amplification/hybridization in microarray-based pooled DNA experiments. Nucleic Acids Research 34, e106. [SCI]




Yang, H.-C., Lin, C.-Y. and Fann, C. S. J.CA (2006/09). A sliding-window weighted linkage disequilibrium test. Genetic Epidemiology 30, 531-545. [SCI]




Wang, R.-Y., Chung, C.-M., Fann, C.S.J., Yang, H.-C., Chen, J.-W., Jong, Y.-S., Jou, Y.-S., Lo, H.-M., Ho, F.-M., Kang, C.-S., Chen, C.-C., Chang, H.-C., Shyue, S.-K. and Pan, W.-H.CA (2007/09). Genome-wide scan for quantitative ACE activity in Taiwan young-onset hypertension study. Human Heredity 65, 85-90. [SCI]




Yang, H.-C.CA, Huang, M.-C., Li, L.-H., Lin, C.-H., Yu, L. T., Diccianni, M. B., Wu, J.-Y., Chen, Y.-T. and Fann, C. S. J.CA (2008/04). MPDA: microarray-based pooled DNA analyzer. BMC Bioinformatics 9, 196. [SCI]




Lian, I.-B., Lin, Y.-H., Lin, Y.-C., Yang, H.-C., Chang, C.-J. and Fann, C. S. J.CA (2008/05). Using the longest significance run to estimate region-specific p-values in genetic association mapping studies. BMC Bioinformatics 9, 246. [SCI]




Yang, H.-C.CA, Hsieh, H.-Y. and Fann, C. S. J. (2008/06). KBAT: Kernel-based association test. Genetics 179, 1057-1068. [SCI]




Zhang, H., Yang, H.-C. and Yang Y.CA (2008/06). PoooL: An efficient method for estimating haplotypes from large DNA pools. Bioinformatics 24, 1942-1948. [SCI]




Huggins, R., Li, L.-H., Lin, Y.-C., Yu, A.L.T. and Yang, H.-C.CA (2008/12). Nonparametric estimation of LOH using Affymetrix SNP genotyping arrays for unpaired samples. Journal of Human Genetics 53, 983-990. [SCI]




Yang, H.-C., Liang, Y.-J., Wu, Y.-L., Chung, C.-M., Chiang, K.-M., Ho, H.-Y., Ting, C.-T., Lin, T.-H., Sheu, S.-H., Tsai, W.-C., Chen, J.-H., Leu, H.-B., Yin, W.-H., Chiu, T.-Y., Chen, C.-I., Fann, C.S.J., Wu, J.-Y., Lin, T.-N., Lin, S.-J, Chen, Y.-T., Chen, J.-W.CA and Pan, W.-H.CA (2009/05). Genome-wide association study of young-onset hypertension in the Han Chinese population of Taiwan. PLoS ONE 4, e5459. [SCI]




Yang, H.-C.CA, Liang, Y.-J., Chung, C.-M., Chen, J.-W. and Pan, W.-H. (2009/12). Genome-wide gene-based association study. BMC Proceedings 3, S135. [PubMed]




Chiu, Y.-F.CA, Kao, H.-Y., Chen, Y.-S., Hsu, F.-C. and Yang, H.-C. (2009/12). Assessment of gene-covariate interactions by incorporating covariates into association mapping. BMC Proceedings 3, S85. [PubMed]




Yang, H.-C.CA, Lin, H.-C., Huang, M.-C., Li, L.-H., Pan, W.-H., Wu, J.-Y. and Chen, Y.-T. (2010/07). A new analysis tool for individual-level allele frequency for genomic studies. BMC Genomics 11, 415. [SCI]




Yang, H.-C.CA, Lin, H.-C., Kang, M., Chen, C.-H., Lin, C.-W., Li, L.-H., Wu, J.-Y., Chen, Y.-T. and Pan, W.-H. (2011/04). SAQC: SNP array quality control. BMC Bioinformatics 12, 100. [SCI]




Yang, H.-C.CA, Chang, L.-C., Huggins, R. M., Chen, C.-H. and Mullighan, C. G. (2011/05). LOHAS: Loss-of-heterozygosity analysis suite. Genetic Epidemiology 35, 247-260. [SCI]




Chung C.-M., Lin, T.-H., Chen, J.-W., Leu, H.-B., Yang, H.-C., Ho, H.-Y., Ting, C.-T., Sheu, S.-H., Tsai, W.-C., Chen, J.-H., Lin, S.-J., Chen, Y.-T. and Pan, W.-H.CA (2011/09). A genome-wide association study reveals a quantitative trait locus of adiponectin on CDH13 that predicts cardiometabolic outcomes. Diabetes 60, 2417-2423. [SCI]




Yang, H.-C.CA and Chen, C.-W. (2011/11). Region-based and pathway-based QTL mapping using a p-value combination method. BMC Proceedings 5, S43. [PubMed]




Yang, H.-C., Liang, Y.-J, Chen, J.-W., Chiang, K.-M., Chung, C.-M., Ho, H.-Y., Ting, C.-T., Lin, T.-H., Sheu, S.-H., Tsai, W.-C., Chen, J.-H., Leu, H.-B., Yin, W.-H., Chiu, T.-Y., Chern, C.-I., Lin, S.-J., Tomlinson, B., Guo, Y., Sham, P. C., Cherny S. S., Lam, T. H., Thomas, G. N. and Pan, W.-H.CA (2012/03). Identification of IGF1, SLC4A4, WWOX and SFMBT1 as hypertension susceptibility genes in Han Chinese population with a genome-wide gene-based association study. PLoS ONE 7, e32907. [SCI]




Lee, S.-C., Yang, Y.-H., Chuang, S.-Y., Liu, S.-C., Yang, H.-C. and Pan, W.-H.CA (2012/03). Risk of asthma associated with energy-dense but nutrient-poor dietary pattern in Taiwanese children. Asia Pacific Journal of Clinical Nutrition 21, 73-81. [SCI]




Yang, H.-C.CA, Chang, L.-C., Liang, Y.-J., Lin, C.-H. and Wang, P.-L. (2012/04). A genome-wide homozygosity association study identifies runs of homozygosity associated with rheumatoid arthritis in the human Major Histocompatibility Complex. PLoS ONE 7, e34840. [SCI]




Yang, H.-C.CA, Wang, P.-L., Lin, C.-W., Chen, C.-H. and Chen, C.-H. (2012/07). Integrative analysis of single nucleotide polymorphisms and gene expression efficiently distinguishes samples from closely related ethnic populations. BMC Genomics 13, 346. [SCI]




Chung, C.-M., Wang, R.-Y., Fann, C.S.J., Chen, J.-W., Jong, Y.-S., Jou, Y.-S., Yang, H.-C., Kang, C.-S., Chen, C.-C.,  Chang, H.-C. and Pan, W.-H.CA (2013/03). Fine-mapping angiotensin-converting enzyme gene: separate QTLs identified for hypertension and for ACE activity. PLoS ONE 8, e56119. [SCI]




Yang, H.-C.EC, Liu, C.-M.EC, Liu, Y.-L., Chen, C.-W., Chang, C. C., Fann, C. S. J., Chiou, J.-J., Yang, Y.-C., Chen, C.-H., Faraone, S. V., Tsuang, M. T. and Hwu, H.-G.CA (2013/03). DAO gene plays an important role on genetic association and interaction to schizophrenia in the Taiwan Han Chinese population. PLoS ONE 8, e60099 [SCI]




Lai, C.-H., Chu, N.-F., Chang, C.-W., Wang, S.-L., Yang, H.-C., Chu, C.-M.CA, Chang, C.-T., Lin, M.-H., Chien, W.-C., Su, S.-L., Chou, Y.-C., Chen, K.-H., Wang, W.-M. and Liou, S.-H. (2013/12). Androgenic alopecia is associated with less dietary soy, higher blood vanadium and rs11603121 polymorphism in Taiwanese communities. PLoS ONE 8, e79789. [SCI]




Yang, H.-C.CA, Lin, C.-W., Chen, C.-W. and Chen, J. J. (2014/04). Applying genome-wide gene-based expression quantitative trait locus mapping to study population ancestry and pharmacogenetics. BMC Genomics 15, 319. [SCI]




Chiang, K.-M., Yang, H.-C., Chen, J.-W., Hwang, S.-M., Ho, H.-Y., Ting, C.-T., Lin, T.-H., Sheu, S.-H., Tsai, W.-C., Chen, J.-H., Leu, H.-B., Yin, W.-H., Chiu, T.-Y., Chen, C.-I., Lin, S.-J., Thomas, N. G., Tomlinson, B., Cherny, S., Gui, H. S., Sham, P. C., Lam, T. H. and Pan, W.-H.CA (2014/06). A three-stage genome-wide association study combining multilocus test and gene expression analysis for young-onset hypertension on Taiwan Han Chinese. American Journal of Hypertension 27, 819-827. [SCI]




Leu, H.-B., Chung, C.-M., Lin, S.-J., Lu, T.-M., Yang, H.-C., Ho, H.-Y., Ting, C.-T., Lin, T.-H., Sheu, S.-H., Tsai, W.-C., Chen, J.-H., Yin, W.-H., Chiu, T.-Y., Chen, C.-I., Pan, W.-H. and Chen, J.-W. (2014/06). A novel SNP associated with nighttime pulse pressure in young-onset hypertension factor for cardiovascular events in a general cohort in Taiwan. PLoS ONE 9, e97919. [SCI]




Yang, H.-C.CA and Li, H.-W. (2014/06). Analysis of homozygosity disequilibrium using whole-genome sequencing data. BMC Proceedings 8, S15. [PubMed]




Leu, H.-B., Chung, C.-M., Lin, S.-J., Chiang, K.-M., Yang, H.-C., Ho, H.-Y., Ting, C.-T., Lin, T.-H., Sheu, S.-H., Tsai, W.-C., Chen, J.-H., Yin, W.-H., Chiu, T.-Y., Chen, C.-I., Fann, C. S. J., Chen, Y.-T., Pan, W.-H. and Chen, J.-W.CA (2015/02). Association of circadian genes with diurnal blood pressure changes and non-dipper essential hypertension: a genetic association with young-onset hypertension. Hypertension Research 38, 155-162. [SCI]




Konig, I. R.CA, Auerbach, J., Gola, D., Held, E., Holzinger, E. R., Legault, M-A, Sun, R. Tintle, N. and Yang, H.-C. (2016/02). Machine learning and data mining in complex genomic data – a review on the lessons learned in Genetic Analysis Workshop 19. BMC Genetics 17, S2. [SCI]




Huang, M.-C., Chuang, T.-P., Chen, C.-H., Wu, J.-Y., Chen, Y.-T., Li, L.-H.CA and Yang, H.-C.CA (2016/03). An integrated analysis tool for hybridization intensities and genotypes using new-generation population-optimized human arrays. BMC Genomics 17, 266. [SCI]




Yang, H.-C., Chu, S.-K., Kuo, H.-W., Wang, S.-C., Liu, S.-W., Ho, I.-K. and Liu, Y.-L.CA (2016/03). Genome-wide pharmacogenomic study on methadone maintenance treatment identifies SNP rs17180299 and multiple haplotypes on CYP2B6, SPON1, and GSG1L associated with plasma concentrations of methadone R- and S-enantiomers in heroin-dependent patients. PLoS Genetics 12, e1005910. [SCI]




Liang, Y.-J., Lin, Y.-T., Chen, C.-W., Lin, C.-W., Chao, K.-M.EC, Pan, W.-H.EC and Yang, H.-C.CA, EC (2016/06). SMART: Statistical Metabolomics Analysis – An R Tool. Analytical Chemistry 88, 6334-6341. [SCI]




Chen, S.-J, Lia, D.-L., Shen, T.-W., Yang, H.-C., Chen, K.-C. and Chen, C.-H.CA (2016/08). Genetic signatures of heroin addiction. Medicine 95, e4473. [SCI]




Yang, H.-C.CA and Lin, Y.-T. (2016/11). Homozygosity disequilibrium and its gene regulation. BMC Proceedings 10, 27. [PubMed] (http://rdcu.be/mHtp)




Chang, H.-C., Chang, H.-Y., Yang, H.-C., Yeh, C.-J. and Pan, W.-H.CA (2017/01). Morbid obesity in Taiwan: Prevalence, trends, associated social demographics, and lifestyle factors. PLoS ONE 12, e01697557. [SCI]




Kuo, H.-W., Shih, C.-L., Tsung, J.-H., Liu, S.-W., Chu, S.-K., Yang, H.-C., Tsou, H.-H., Wang, Z.-H., Chen, Andrew, C. H. and Liu, Y.-L.CA (2017/03). Pharmacogenomics study on cadherin 2 network with regard to HIV infection and methadone treatment outcome. PLoS ONE 12, e0174647. [SCI]




Yang, H.-C., Chen, I.-C., Tsay, Y.-C., Li, Z.-R., Chen, C.-H., Hwu, H.-G. and Chen, C.-H.CA (2017/04). Using an event-history with risk-free model to study the genetics of alcoholism. Scientific Report 7, 1975. [SCI] (http://rdcu.be/r18K)


- Book Chapters




Chao, A.CA, Yang, H.-C. and Yip, P. S. F. (2003). The use of capture-recapture methodology in epidemiological surveillance. pp. 711-739 in Y. Lu and J.-Q. Fang (Ed.), Advanced Medical Statistics. World Scientific Publishing Company, Singapore.




Yang, H.-C. and Fann, C. S. J.CA (2007). Association mapping using pooled DNA. pp. 161-175 in A. R. Collins (Ed.), Linkage Disequilibrium and Association Mapping, The Humana Press Inc., USA.




Chao, A.CA, Hsieh T. C. and Yang, H.-C. (2015). The use of capture-recapture methodology in epidemiological surveillance and ecological surveys. pp. 425-467 in Y. Lu, J.-Q. Fang, L. Tian and H. Jin (Ed.), Advanced Medical Statistics. 2nd Edition. World Scientific Publishing Company, Singapore.



- Scientific Reports




Geffers, J., Beaudry, C., Yang, H.-C., Huang, F., Phanraksa, O., Dominik, M., Lin, Y.-C., Huang, M.-C., Komai, S., Lorimer, K., Piyawattanametha, W., Saengchantr, P., Saleh, H., Tagg, B. and Veerakumarasivam, A. (2017/01). Global State of Young Scientists (GloSYS) in ASEAN – Creativity and Innovation of Young Scientists in ASEAN. Editor: Global Young Academy. Halle, Germany (ISBN: 978-3-8047-3709-9).



- Software and Database




CARE-2 (Capture-Recapture Part 2)

Website: http://chao.stat.nthu.edu.tw/wordpress/software_download/




CARE-4 (Capture-Recapture Part 4)

Website: http://chao.stat.nthu.edu.tw/wordpress/software_download/




Database of CPA (Coefficient of Preferential Amplification/Hybridization)  

Website: http://www.ibms.sinica.edu.tw/~csjfann/first flow/database.htm




PDA (Pooled DNA Analyzer)  

Website: http://www.csjfann.ibms.sinica.edu.tw/EAG/Program/PDA/Pda.php




KBAT (Kernel-Based Association Test)

Website: http://www.stat.sinica.edu.tw/hsinchou/genetics/association/KBAT.htm




MPDA (Microarray Pooled DNA Analyzer)

Website: http://www.stat.sinica.edu.tw/hsinchou/genetics/pooledDNA/mpda.htm




ALOHA (Allele-Frequency/Loss-of-Heterozygosity/Allelic-Imbalance)

Website: http://www.stat.sinica.edu.tw/hsinchou/genetics/aloha/ALOHA.htm




AF database and CPA database





LOHAS (Loss-Of-Heterozygosity Analysis Suite)

Website: http://www.stat.sinica.edu.tw/hsinchou/genetics/loh/LOHAS.htm


SAQC (SNP Array Quality Control)

Website: http://www.stat.sinica.edu.tw/hsinchou/genetics/quality/SAQC.htm


BIASLESS (Biomarkers Identification And Samples Subdivision)

Website: http://www.stat.sinica.edu.tw/hsinchou/genetics/prediction/BIASLESS.htm




Program and databases of gene-based eQTL (expression Quantitative Trait Loci)

Website: http://www.stat.sinica.edu.tw/hsinchou/genetics/eQTL/HapMapII.htm





Website: http://hcyang.stat.sinica.edu.tw/software/ALICE.html




SMART (Statistical Metabolomics Analysis An R Tool)

Website: http://www.stat.sinica.edu.tw/hsinchou/metabolomics/SMART.htm




·           Others.pdf