Research interests

Statistical Genetics, Genetic data analysis

Rapid development of biomedical data profiling techniques has prompted unprecedented growth of data science in medicine. Shih-Kai's research focuses on studying statistical and computational methods in high-dimensional biomedical data analysis, and the results in human genetic data have showed (1) a guideline to select suitable noise reduction methods for single-cell RNA sequencing data; (2) computational algorithms to prioritize pathogenic variants for medical genetic data; (3) key genes associated with the treatment response in heroin-dependence patients or with interethnic effects in pharmaco-epigenetics. His current research conducts integrative analysis of genomic and medical imaging data by machine learning methods.

Education

2010-2017 Ph.D., Bioinformatics Program, Taiwan International Graduate Program, Academia Sinica, Taiwan

2004-2006 M.S., Department of Statistics, National Taipei Uniersity, Taiwan

2000-2004 B.S., Department of Applied Mathematics, National Cheng-chi University, Taiwan

Professional Experience

2023.08-present Assistant Professor; Department of Statistics, 

National Taipai University, Taiwan

2021.09-2023.07 Postdoctoral Research Fellow; Institute of Statistical Science, 

Academia Sinica, Taiwan

2020.11-2021.09 Assistant Research Fellow; Clinical Medicine Research Center, 

National Cheng Kung University Hospital, Taiwan

2018.09-2020.08 Postdoctoral Research Fellow; Department of Biostatistics, 

Vanderbilt University Medical Center, TN USA

2010.09-2018.01 Research Assistant; Institute of Statistical Science, 

Academia Sinica, Taiwan

2008.09-2010.08 Research Assistant; Institute of Statistical Science, 

Academia Sinica, Taiwan

2007.01-2007.09 Research Assistant; HIV/AIDS department, 

Centers for Disease Control, Taiwan

Publications

(*Corresponding Author)

Ya-Ting Hsu, Li-Hsien Chen, Ya-Hui Liu, Shih-Kai Chu, Tsai-Yun Chen, Kuen-Jer Tsai,  Meng-Ru Shen*, Wentai Liu*. Electrical Sympathetic Neuromodulation Protects Bone Marrow Niche and Drives Hematopoietic Regeneration during Chemotherapy. Small Methods. 7(6):e2201300, 2023 June

Meng-Che Tsai, Chih-Hui Hsu, Shih-Kai Chu, Marie-Hélène Roy-Gagnon, Sheng-Hsiang Lin*. Genome-wide association study of age at menarche in the Taiwan Biobank suggests NOL4 as a novel associated gene. Journal of Human Genetics. 68(5):339-345, 2023 May

Shih-Kai Chu, Shilin Zhao, Yu Shyr*, Qi Liu*. Comprehensive evaluation of noise reduction methods for single-cell RNA sequencing data. Briefings in Bioinformatics. 23(2):bbab565, 2022 March

Hsin-Chou Yang*, Chia-Wei Chen, Yu-Ting Lin, Shih-Kai Chu. Genetic ancestry plays a central role in population pharmacogenomics. Communications Biology. 4(1):171, 2021 February

Satya Das*, Kristen K. Ciombor, Sigurdis Haraldsdottir, Yoanna Pumpalova, Ibrahim H. Sahin, G. Pineda, Yu Shyr, E.P. Lin, Chih-Yuan Hsu, Shih-Kai Chu, Laura W. Goff, Dana B. Cardin, Mehmet A. Bilen, George A. Fisher, Christina Wu, Jordan Berlin. Immune‐Related Adverse Events and Immune Checkpoint Inhibitor Efficacy in Patients with Gastrointestinal Cancer with Food and Drug Administration‐Approved Indications for Immunotherapy. The Oncologist. 25(8):669-679, 2020 August

Shih-Kai Chu, Hsin-Chou Yang*. Interethnic DNA methylation difference and its implications in pharmacoepigenetics. Epigenomics. 9(11):1437-1454, 2017 November

Hsiang-Wei Kuo, Chia-Lung Shih, Jieh-Hen Tsung, Sheng-Wen Liu, Shih-Kai Chu, Hsin-Chou Yang, Hsiao-Hui Tsou, Zih-Hsiang Wang, Andrew C. H. Chen, Yu-Li Liu*. Pharmacogenomics study on cadherin 2 network with regard to HIV infection and methadone treatment outcome. PLoS ONE. 12(3):e0174647, 2017 March

Hsin-Chou Yang, Shih-Kai Chu, Chieh-Liang Huang, Hsiang-Wei Kuo, Sheng-Chang Wang, Sheng-Wen Liu, Ing-Kang Ho, Yu-Li Liu*. 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(3):e1005910, 2016 March

Yi-Ting Hwang*, Shih-Kai Chu, Shyh-Tyan Ou. Evaluations of FDR-controlling procedures in multiple hypothesis testing. Statistics and Computing. 21:569–83, 2011 October