Publications
Evolution on Infectious Diseases
Unpacking the spread of pathogens
Hsueh-Chien Raymond Cheng*, Diego Teixeira
Nature Reviews Microbiology, 2025.
Genomic analysis of the Streptococcus pneumoniae in Taiwan: a nationwide study from 2006 to 2022
Hsueh-Chien Raymond Cheng*, Shu-Chen Kuo, Jui-Fen Lai, Han-Chieh Wu, Feng-Jui Chen, Huey-Kang Sytwu, Stephanie W. Lo, Stephen D. Bentley and Ying-Chi Huang
Microbial Genomics, 2025.
Geographical structure and evolutionary trajectories of Streptococcus pneumoniae serotype 19F lineages in South Africa
Antidius R Laurian, Hsueh-Chien Raymond Cheng, Takudzwa Matuvhunye, Celine De Allende, Kate C Mellor, Heather J Zar, Mark Nicol, Stephen D Bentley, Stephanie W Lo, Felix S Dube
MedRxiv, 2025.
Estimating geographical spread of Streptococcus pneumoniae within Israel using genomic data
Hsueh-Chien Raymond Cheng*, Sophie Belman, Henrik Salje, Ron Dagan & Stephen D Bentley
Microbial Genomics, 2024.
Post-vaccine epidemiology of serotype 3 pneumococci identifies transformation inhibition through prophage-driven alteration of a non-coding RNA
Min Jung Kwun, Alexandru V. Ion, Hsueh-Chien Cheng*, Joshua C. D’Aeth, Sam Dougan, Marco R. Oggioni, David A. Goulding, Stephen D. Bentley & Nicholas J. Croucher
Genome Medicine, 2022.
Evolution on Human Genetics
Detecting Genetic Ancestry and Adaptation in the Taiwanese Han People
Yun-Hua Lo, Hsueh-Chien Cheng*, Chia-Ni Hsiung, Show-Ling Yang, Han-Yu Wang, Chia-Wei Peng, Chun-Yu Chen, Kung-Ping Lin, Mei-Ling Kang, Chien-Hsiun Chen, Hou-Wei Chu, Chiao-Feng Lin, Mei-Hsuan Lee, Quintin Liu, Yoko Satta, Cheng-Jui Lin, Marie Lin, Shu-Miaw Chaw, Jun-Hun Loo, Chen-Yang Shen, Wen-Ya Ko
Molecular Biology and Evolution, 2021.
Whole Genome Assembly
A novel genome optimization tool for chromosome-level assembly across diverse sequencing techniques
Wei-Hsuan Chuang, Hsueh-Chien Cheng, Yu-Jung Chang, Pao-Yin Fu, Yi-Chen Huang, Ping-Heng Hsieh, Shu-Hwa Chen, Pui-Yan Kwok, Chung-Yen Lin, Jan-Ming Ho
bioRxiv, 2023.
Machine Learning on Health
Screening for obstructive sleep apnea risk by using machine learning approaches and anthropometric features
Cheng-Yu Tsai, Huei-Tyng Huang, Hsueh-Chien Cheng, Jieni Wang, Ping-Jung Duh, Wen-Hua Hsu, Marc Stettler, Yi-Chun Kuan, Yin-Tzu Lin, Chia-Rung Hsu, Kang-Yun Lee,
Jiunn-Horng Kang & Wen-Te Liu
Sensors, 2022.