| Issue Date | Title | Author(s) | Relation | scopus | WOS | Fulltext/Archive link |
| 2014 | A comprehensive resource of genomic, epigenomic and transcriptomic sequencing data for the black truffle Tuber melanosporum | Pao-Yang Chen; Barbara Montanini; Wen-Wei Liao; Marco Morselli; Artur Jaroszewicz; David Lopez; Simone Ottonello; Matteo Pellegrini | GigaScience 3(25) | | | |
| 2018 | BS-Seeker3: Ultrafast pipeline for bisulfite sequencing | Yu Yuan Huang; Yan-Jiun Huang; Pao-Yang Chen | BMC Bioinformatics 19, 111 | | | |
| 2018 | Chapter 4 - Bioinformatics of Epigenomic Data Generated From Next-Generation Sequencing | Fei-Man Hsu; Moloya Gohain; Pearl Chang; Jui-Hsien Lu; Pao-Yang Chen | Epigenetics in Human Disease (Second Edition) Volume 6 in Translational Epigenetics (USA : Elsevier Inc. Academic Press) | | | |
| 2018 | Computational Methods for Assessing Chromatin Hierarchy | Pearl Chang; Moloya Gohain; Ming-Ren Yen; Pao-Yang Chen | Computational and Structural Biotechnology Journal 16, 43-53 | | | |
| 2015 | DNA Demethylation Dynamics in the Human Prenatal Germline | Sofia Gkountela; Kelvin Zhang; Tiasha Shafiq; Wen-Wei Liao; Joseph Hargan-Calvopina; Pao-Yang Chen; Amander T Clark | CELL 161(6), 1425-1436 | | | |
| 2018 | Dynamics of the Methylome and Transcriptome during the Regeneration of Rice | Fei-Man Hsu; Moloya Gohain; Archana Allishe; Yan-Jiun Huang; Jo-Ling Liao; Lin-Yun Kuang; Pao-Yang Chen | Epigenomes 2(3), 14 | | | |
| 2015 | Epigenetic reprogramming in the mammalian germline | Fei-Man Hsu; Amander Clark; Pao-Yang Chen | Oncotarget 6(34), 35151-35152 | | | |
| 2015 | MethGO: a comprehensive tool for analyzing whole genome bisulfite sequencing data | Ming-Ren Yen; Wen-Wei Liao; Evaline Ju; Fei-Man Hsu; Larry Lam; Pao-Yang Chen | BMC GENOMICS 16(Suppl 12):S11 | | | |
| 2016 | Profiling genome-wide DNA methylation | Wai-Shin Yong; Fei-Man Hsu; Pao-Yang Chen | Epigenetics & Chromatin 9, 26 | | | |
| 2016 | TEA: the epigenome platform for Arabidopsis methylome study | Sheng-Yao Su; Shu-Hwa Chen; I-Hsuan Lu; Yih-Shien Chiang; Yu-Bin Wang; Pao-Yang Chen; Chung-Yen Lin | BMC GENOMICS 17(Suppl 13), 1027 | | | |
| 2018 | Using flow cytometry to isolate maize meiocytes for next generation sequencing: A time and labor efficient method | Pearl Chang; Yu-Fang Tseng; Pao-Yang Chen; Chung-Ju Rachel Wang | Current Protocols in Plant Biology 3(2), e20068 | | | |
| 2016 | Views on Profiling Genomewide DNA Methylation and Crop Methylomes | Fei-Man Hsu; Wai-Shin Yong; Pao-Yang Chen | Crop, Environment & Bioinformatics 13, 39-51 | | | |
