| Issue Date | Title | Author(s) | Relation | scopus | WOS | Fulltext/Archive link |
| 2017 | A termite symbiotic mushroom maximizing sexual activity at growing tips of vegetative hyphae | Huei-Mei Hsieh; Mei-Chu Chung ; Pao-Yang Chen ; Fei-Man Hsu; Wen-Wei Liao; Ai-Ning Sung; Chun-Ru Lin; Chung-Ju Wang ; Yu-Hsin Kao; Mei-Jane Fang; Chi-Yung Lai; Chieh-Chen Huang; Jyh-Ching Chou; Wen-Neng Chou; Bill Chia-Han Chang; Yu-Ming Ju | Botanical Studies 58, 39 | | | |
| 2022 | Aberrant overexpression of HOTAIR inhibits abdominal adipogenesis through remodelling of genome-wide DNA methylation and transcription | Kuo, FC; Huang, YC; Yen, MR; Lee, CH; Hsu, KF; Yang, HY; Wu, LW; Lu, CH; Hsu, YJ; Chen, PY | Molecular metabolism 60, 101473 | | | |
| 2021 | ATACgraph: Profiling Genome-Wide Chromatin Accessibility From ATAC-seq | Rita Jui-Hsein Lu; Yen-Ting Liu; Chih Wei Huang; Ming-Ren Yen; Chung-Yen Lin ; Pao-Yang Chen | FRONTIERS IN GENETICS 11, 618478 | | | |
| 2019 | Behavioral Epigenetics: Perspectives Based on Experience-Dependent Epigenetic Inheritance | Pang, YY; Lu, JH; Chen, PY | Epigenomes 3(3), 18 | | | |
| 2024 | Bioinformatics Analysis of DNA Methylation | Lin, PY; Chen, KL; Lin, GJ; Huang, SC; Chen, PY | Methods in Molecular Biology (Springer Nature) | | | |
| 2022 | Blimp-1 molds the epigenetic architecture of IL-21–mediated autoimmune diseases through an autoregulatory circuit | Liu, YW; Fu, SH; Chien, MW; Hsu, CY; Lin, MH; Dong, JL; Lu, RJ; Lee, YJ; Chen, PY ; Wang, CH; Sytwu, HK | JCI insight 7(11), e151614 | | | |
| 2013 | BS-Seeker2: a versatile aligning pipeline for bisulfite sequencing data. | Guo, W; Fiziev, P; Yan, W; Cokus, S; Sun, X; Zhang, MQ; Chen, PY ; Pellegrini, M | BMC genomics 14, 774 | | | |
| 2022 | BSImp: Imputing Partially Observed Methylation Patterns for Evaluating Methylation Heterogeneity | Chang, YT; Yen, MR; Chen, PY | Frontiers in Bioinformatics 2, 815289 | | | |
| 2024 | Chapter 3 - Bioinformatics of epigenetic data generated from next-generation sequencing | Sheu, CY L; Huang, YC; Lin, PY; Lin, GJ; Chen, PY | Epigenetics in Human Disease (Third Edition) (United Kingdom : Elsevier) | | | |
| 2020 | Construction and characterization of a knock-down RNA interference line of OsNRPD1 in rice (Oryza sativa ssp japonica cv Nipponbare) | Debladis, Emilie; Lee, Tzuu-Fen; Huang, Yan-Jiun; Lu, Jui-Hsien; Mathioni, Sandra M.; Carpentier, Marie-Christine; Llauro, Christel; Pierron, Davy; Mieulet, Delphine; Guiderdoni, Emmanuel; Chen, Pao-Yang ; Meyers, Blake C.; Panaud, Olivier; Lasserre, Eric | Philosophical Transactions of the Royal Society B: Biological Sciences 375(1795), 20190338 | | | |
| 2019 | Detecting and prioritizing biosynthetic gene clusters for bioactive compounds in bacteria and fungi. | Tran, PN; Yen, MR; Chiang, CY; Lin, HC ; Chen, PY | Applied microbiology and biotechnology 103(8), 3277-3287 | | | |
| 2023 | Detecting the Interplay Between DNA Methylation and Lipid Production in Plants | Hsieh, JW; Liu, YC; Huang, LT; Nakamura, Y; Chen, PY | | | | |
| 2017 | Deubiquitinating Enzyme OTU5 Contributes to DNA Methylation Patterns and Is Critical for Phosphate Nutrition Signals. | Yen, MR; Suen, DF; Hsu, FM; Tsai, YH; Fu, H; Schmidt, W; Chen, PY | Plant physiology 175(4), 1826-1838 | | | |
| 2021 | Dissecting the Dynamic Changes of Methylome During Rice Transformation | Chen, PY | | | | |
| 2014 | Distinct and concurrent pathways of Pol II- and Pol IV-dependent siRNA biogenesis at a repetitive trans-silencer locus in Arabidopsis thaliana. | Sasaki, T; Lee, TF; Liao, WW; Naumann, U; Liao, JL; Eun, C; Huang, YY; Fu, JL; Chen, PY ; Meyers, BC; Matzke, AJ; Matzke, M | The Plant journal : for cell and molecular biology 79(1), 127-38 | | | |
| 2021 | Diversity of Fungal DNA Methyltransferases and Their Association With DNA Methylation Patterns | Nai, YS; Huang, YC; Yen, MR; Chen, PY | Frontiers in microbiology 11, 616922 | | | |
| 2022 | EED is required for mouse primordial germ cell differentiation in the embryonic gonad | Lowe, MG; Yen, MR; Hsu, FM; Hosohama, L; Hu, Z; Chitiashvili, T; Hunt, TJ; Gorgy, I; Bernard, M; Wamaitha, SE; Chen, PY ; Clark, AT | Developmental cell 57(12), 1482-1495.e5 | | | |
| 2022 | Epigenome Bioinformatics in Plants | Chen, PY | | | | |
| 2022 | Epigenome bioinformatics in rice and plants | Chen, PY | | | | |
| 2023 | Epigenomic Footprints in the Regeneration and Transformation of Rice | Hsieh, JW A; Chang, P; Kuang, LY; Hsing, YI, C; Chen, PY | | | | |
