Epigenomes in plants, animals and fungi
動、植物及真菌的基因體及表觀遺傳基因體
Pao-Yang Chen's Laboratory
陳柏仰實驗室
Pao-Yang Chen's Laboratory
陳柏仰實驗室
Next-generation or massively parallel DNA sequencing technologies have the potential to markedly accelerate genetics and epigenetics research. Our lab utilizes the next-generation sequencing technique to establish genome-wide DNA methylation profiles, investigate chromatin accessibility and histone modifications, and process transcriptome analysis. These results from next-generation sequencing allow us to explore the epigenetic patterns, and the correlation between epigenome and gene expression of plants, fungi, and human. Our research is to integrate both experiments and statistical methods and bioinformatic software to address biologically relevant questions.
表觀遺傳是在不改變DNA序列的情況下，透過修飾染色質結構或轉錄後調控，影響基因表現並導致性狀改變 ，甚至遺傳給後代，常見的機制包含DNA甲基化、組蛋白修飾、小分子RNA等。近年來隨著次世代定序技術的發展，使我們得以探索全基因 體中，每個鹼基對的表觀遺傳修飾情形，進而解答許多遺傳學無法解釋的問題。本實驗室專長表觀遺傳研究並首重DNA甲基化，利用次世代定序建立全基因體的DNA甲基化圖譜，來深入了解植物、真菌、人類的DNA甲基化與其對基因表現的影響。在完成生物樣本的建庫後，我 們針對次世代定序所產生的龐大資料，研究統計方法，並發展計算工具，以解讀生物學上相關的問題。
開發生物資訊工具有助於分析整個基因體的表觀遺傳修飾，以更全面地了解基 因調控及其在動植物發育、人類疾病和環境逆境中的作用。實驗室結合程式語言的能力和對於生物學的知識，建立了多種生物資訊相關工具和網站，包含上游資料處理工具能夠將甲基化的序列回貼基因體上，可以更快速地得到可分析的甲基化資料；下游的全基因體甲基化資 料分析或是染色質的開放程度分析，讓其他使用者可以運用簡單的操作就得到生物體中不同表觀遺傳修飾的程度與差異度在不同位點之間 的分析結果；甚至是與基因表現之間的關聯性分析或是甲基化異質性的計算，將統計與數學模型應用在表觀遺傳學的分析中，以全新的方 法來更準確的了解表觀遺傳修飾在生物體中的作用與表現，以提升表觀遺傳研究的發展。
To comprehensively understand epigenomics in plants, animals and fungi. We combine the skills for programming and the knowledge for biology to develop multiple bioinformatics tools and websites. For example, we established tools which can align methylated sequences, efficiently providing the usable data for the analyses; as well as various comprehensive genome-wide epigenomics data analysis, such as methylation level assessment, chromatin accessibility evaluation, and differentially analysis for identifying the critical regions and genes. Additionally, we applied the statistical and mathematical models to analyse the correlation between epigenetic modifications and gene expression, or calculating methylation heterogeneity to gain more accurate results and precise insights. These tools allow the researcher to enhance the efficiency of epigenomics research, contributing to the continuous advancement of this field.
植物和動物的基因組DNA甲基化遺傳標記隱藏著很重要的生物學意義。我們的實驗室與國內外多個實驗室有 合作計畫，共同研究各樣植物和動物的DNA甲基化模式。例如，我們希望對基因改良的水稻基因體及表觀基因體進行詳細的研究分析。這個結果將增進水稻基因改良的品質以及轉殖的效率。藉由檢視阿拉伯芥甲基轉移酶參與調控網路與脂質生成調控網路的基因體、表觀基因 體與轉錄體間的比較，我們辨識出調控植物油品質的關鍵基因群。 未來將進一步以阿拉伯芥的研究成果作為基礎，進而研究提高產油植物油產量與品質的應用。 糖尿病是現代文明病之一，其中第二型糖尿病能以藥物進行治療。透過比較糖尿病患者服用藥物前後，可以評估基因體甲基化變化治療效果。 初步結果顯示治療後第二型糖尿病患者的基因體甲基化模式有向一般人的基因體甲基化模式接近的趨勢 ，顯示治療效果帶來表觀遺傳層級的改變。我們在人類生殖細胞的表觀基因體研究，發表了人類第一個表觀基因體重置的圖譜，是一重大 突破，我們並展開一連串的相關研究，探討此遺傳上獨特且重要的細胞。新的定序技術讓我們可以分析生物全基因體的DNA甲基化模式。透過基因體、表觀基因體與轉錄體的相互比較提供多層次的觀點，以利深入生物議題的探究。
Pei-Yu Lin, Shiang-Chin Huang, Kuan-Lin Chen, Yu-Chun Huang, Chia-Yu Liao, Guan-Jun Lin, HueyTyng Lee, and Pao-Yang Chen (2025) Analysing Protein Complexes in Plant Science: Insights and limitation with AlphaFold 3. Botanical Studies, Accepted.
Kuan-Ting Hsin, HueyTyng Lee, Yu-Chun Huang, Guan-Jun Lin, Pei-Yu Lin, Ying-Chung Jimmy Lin, and Pao-Yang Chen (2025) Lignocellulose Degradation in Bacteria and Fungi: Cellulosomes and Industrial Relevance. Frontiers in Microbiology, 16, 1583746. https://doi.org/10.3389/fmicb.2025.1583746 (Part of the Research Topic “Recent Advances in Cellulosomes and Their Application in Bioenergy Production”)
Debamalya Chatterjee, Ziru Zhang, Pei-Yu Lin, Po-Hao Wang, Gurpreet K Sidhu, Neela H Yennawar, Jo-Wei Allison Hsieh, Pao-Yang Chen, Rentao Song, Blake C. Meyers, and Surinder Chopra (2025) Maize unstable factor for orange1 Encodes a Nuclear Protein that Affects Redox Accumulation During Kernel Development. The Plant Cell, koae301. https://doi.org/10.1093/plcell/koae301
Chih-Hung Hsieh, Ya-Ting Sabrina Chang, Ming-Ren Yen, Jo-Wei Allison Hsieh and Pao-Yang Chen (2024) Predicting protein synergistic effect in Arabidopsis using epigenome profiling. Nature Communications, 15, 9160. https://doi.org/10.1038/s41467-024-53565-y
Jo-Wei Allison Hsieh, Ming-Ren Yen, Fu-Yu Hung, Keqiang Wu* and Pao-Yang Chen* (2024) Epigenetic-driven synergistic and antagonistic regulation on transposable elements by HDA6 and LDL1/LDL2 in Arabidopsis. Plant Physiology, kiae392. https://doi.org/10.1093/plphys/kiae392
Ti-Wen Lu, Wen-Huei Chen, Pao-Yang Chen, Yu-Chen Shu, Hong-Hwa Chen (2024) Perturbation of periodic spot-generation balance leads to diversified pigmentation patterning of harlequin Phalaenopsis orchids: in silico prediction. BMC Plant Biology, 24, 681. https://doi.org/10.1186/s12870-024-05305-z
Jo-Wei Allison Hsieh☨, Pei-Yu Lin☨, Chi-Ting Wang, Yi-Jing Lee, Pearl Chang, Rita Jui-Hsien Lu, Pao-Yang Chen*, Chung-Ju Rachel Wang* (2024) Establishing an optimized ATAC-seq protocol for the maize. Frontiers in Plant Science, Sec. Plant Genetics, Epigenetics and Chromosome Biology, 15. https://doi.org/10.3389/fpls.2024.1370618
Pei-Yu Lin, Kuan-Lin Chen, Guan-Jun Lin, Shiang-Chin Huang and Pao-Yang Chen (2024) Bioinformatics Analysis of DNA Methylation. Methods in Molecular Biology, DNA methylation edition, Springer Nature, Accepted.
Fei-Man Hsu, Pao-Yang Chen and Matteo Pellegrini (2024) Whole Genome Bisulfite Sequencing. Methods in Molecular Biology, DNA methylation edition, Springer Nature, Accepted.
Chiao-Yu Lyra Sheu☨, Yu-Chun Huang☨, Pei-Yu Lin, Guan-Jun Lin, Pao-Yang Chen (2024) Chapter 3: Bioinformatics of epigenetic data generated from next-generation sequencing. Epigenetics in Human Disease, Elsevier, 3rd Edition, p. 37-82. ISBN: 9780443218125
Pei-Yu Lin☨, Ya-Ting Sabrina Chang☨, Yu-Chun Huang, Pao-Yang Chen (2023) Estimating genome-wide DNA methylation heterogeneity with methylation patterns. Epigenetics & Chromatin, 16, 44. https://doi.org/10.1186/s13072-023-00521-7 Github
HueyTyng Lee, Pei-Yu Lin, Pao-Yang Chen (2023) There’s More to It: Uncovering Genomewide DNA Methylation Heterogeneity. Epigenomics, 15(13), 687–691. https://doi.org/10.2217/epi-2023-0228
Jo-Wei Allison Hsieh, Pearl Chang, Lin-Yun Kuang, Yue-Ie Hsing, Pao-Yang Chen (2023) Rice transformation treatments leave specific epigenome changes beyond tissue culture. Plant Physiology, kiad382. https://doi.org/10.1093/plphys/kiad382.
Ya-Ting Sabrina Chang, Ming-Ren Yen, Pao-Yang Chen (2023) Methylome Imputation by Methylation Patterns. Computational Epigenomics and Epitranscriptomics. Methods Mol Biol., p. 115-126. https://doi: 10.1007/978-1-0716-2962-8_8. Github
Rita Jui-Hsien Lu☨, Pei-Yu Lin☨, Ming-Ren Yen☨, Bing-Heng Wu, Pao-Yang Chen (2023) MethylC-analyzer: a comprehensive downstream pipeline for the analysis of genome-wide DNA methylation. Botanical Studies, 64, 1. https://doi.org/10.1186/s40529-022-00366-5 Github Dockerhub
Pierre Bourguet, Ramesh Yelagandula, Taiko Kim To, Akihisa Osakabe, Archana Alishe, Rita Jui-Hsien Lu, Tetsuji Kakutani, Pao-Yang Chen*, Frédéric Berger* (2022) The histone variant H2A.W cooperates with chromatin modifications and linker histone H1 to maintain transcriptional silencing of transposons in Arabidopsis. bioRxiv, 2022-05. https://doi.org/10.1101/2022.05.31.493688
Yi-Tsung Tu, Chia-Yang Chen, Yi-Sui Huang, Chung-Han Chang, Ming-Ren Yen, Jo-Wei Allison Hsieh, Pao-Yang Chen* and Keqiang Wu* (2022) HISTONE DEACETYLASE 15 and MOS4-Associated Complex subunits 3A/3B coregulate intron retention of ABA-responsive genes. Plant Physiology, 190(1), 882-897. https://doi.org/10.1093/plphys/kiac271
Matthew Lowe, Ming-Ren Yen, Fei-Man Hsu, Linzi Hosohama, Zhongxun Hu, Tsotne Chitiashvili, Timothy Hunt, Isaac Gorgy, Matthew Bernard, S Wamaitha, Pao-Yang Chen*, Amander Ｔ Clark* (2022) EED is required for Mouse Primordial Germ Cell Differentiation in the Embryonic Gonad. Developmental Cell, 57(12), 1482-1495. https://doi.org/10.1016/j.devcel.2022.05.012
Yu-Wen Liu, Shin-Huei Fu, Ming-Wei Chien, Chao-Yuan Hsu, Ming-Hong Lin, Jia-Ling Dong, Rita Jui-Hsien Lu, Yi-Jing Lee, Pao-Yang Chen, Chih-Hung Wang, and Huey-Kang Sytwu (2022) Blimp-1 moulds the epigenetic architecture of IL-21-mediated autoimmune diseases through an autoregulatory circuit. JCI Insight, 7(11). https://doi.org/10.1172/jci.insight.151614
Feng-Chih Kuo*, Yu-Chun Huang, Ming-Ren Yen, Chien-Hsing Lee, Kuo-Feng Hsu, Hsiang-Yu Yang, Li-Wei Wu, Chieh-Hua Lu, Yu-Juei Hsu, Pao-Yang Chen* (2022) Aberrant overexpression of HOTAIR inhibits abdominal adipogenesis through remodelling of genome-wide DNA methylation and transcription. Molecular Metabolism, 60, 101473. https://doi.org/10.1016/j.molmet.2022.101473
Ya-Ting Sabrina Chang, Ming-Ren Yen, Pao-Yang Chen (2022) BSImp: imputing partially observed methylation patterns for evaluating methylation heterogeneity. Frontiers in Bioinformatics, 2, 815289. Research Topic in Computational Methods for Analysis of DNA Methylation Data. https://doi: 10.3389/fbinf.2022.815289 (featured in Editorial)
Pei-Yu Lin and Pao-Yang Chen (2021) Review of: Deep-BGCpred: A unified deep learning genome-mining framework for biosynthetic gene cluster prediction. Qeios. https://doi.org/10.32388/14X8U9
Chih-Yi Yang☨, Rita Jui-Hsien Lu☨, Ming-Kang Lee☨, Shih-Hsiang Felix Hsiao, Ya-Ping Yen, Chun-Chun Cheng, Pu-Sheng Hsu, Yi-Tzang Tsai, Shih-Kuo Chen, I-Hsuan Liu, Pao-Yang Chen*, Shau-Ping Lin* (2021) Transcriptome Analysis of Dnmt3l Knock-Out Mice Derived Multipotent Mesenchymal Stem/Stromal Cells During Osteogenic Differentiation. Frontiers in Cell and Developmental Biology, section Stem Cell Research. https://doi.org/10.3389/fcell.2021.615098
Yu-Shin Nai☨, Yu-Chun Huang☨, Ming-Ren Yen, Pao-Yang Chen (2021) Diversity of fungal DNA methyltransferases and their association with DNA methylation patterns. Frontiers in Microbiology, section Evolutionary and Genomic Microbiology. https://doi.org/10.3389/fmicb.2020.616922
Rita Jui-Hsein Lu☨, Yen-Ting Liu☨, Chih Wei Huang☨, Ming-Ren Yen, Chung-Yen Lin, Pao-Yang Chen (2021) ATACgraph: profiling genome wide chromatin accessibility from ATAC-seq. Frontiers in Genetics, section Epigenomics and Epigenetics. https://doi.org/10.3389/fgene.2020.618478 Github
Huei-Mien Ke, Hsin-Han Lee, Chan-Yi Ivy Lin, Yu-Ching Liu, Min R. Lu, Jo-Wei Allison Hsieh, Chiung-Chih Chang, Pei-Hsuan Wu, Meiyeh Jade Lu, Jeng-Yi Li, Gaus Shang, Rita Jui-Hsien Lu, László G. Nagy, Pao-Yang Chen, Hsiao-Wei Kao and Isheng Jason Tsai (2020) Mycena genomes resolve the evolution of fungal bioluminescence. Proceedings of the National Academy of Sciences, 117(49), 31267-31277. https://doi.org/10.1073/pnas.2010761117
Fu-Yu Hung, Chen Chen, Ming-Ren Yen, Jo-Wei Allison Hsieh, Chenlong Li, Yuan-Hsin Shih, Fang-Fang Chen, Pao-Yang Chen*, Yuhai Cui*, Keqiang Wu* (2020) The expression of long noncoding RNAs is associated with H3Ac and H3K4me2 changes regulated by the HDA6-LDL1/2 histone modification complex in Arabidopsis. NAR Genomics and Bioinformatics, Vol 2, Issue 3, lqaa066. https://doi.org/10.1093/nargab/lqaa066
Hong Zhu, Pao-Yang Chen, Silin Zhong, Christopher Dardick, Ann Callahan, Yong-Qiang An, Steve van Nocker, Yingzhen Yang, Gan-Yuan Zhong, Albert Abbott, Zongrang Liu (2020) Thermal-responsive genetic and epigenetic regulation of DAM cluster controlling dormancy and chilling requirement in peach floral buds. Horticulture Research, 7, 114. https://doi.org/10.1038/s41438-020-0336-y
Jo-Wei Allison Hsieh, Ming-Ren Yen, Pao-Yang Chen (2020) Epigenomic regulation of OTU5 in Arabidopsis thaliana. Genomics, 112(5): 3549-3559. https://doi.org/10.1016/j.ygeno.2020.04.006
Chin-Sheng Teng, Bing-Heng Wu, Ming-Ren Yen, Pao-Yang Chen (2020) MethGET: web-based bioinformatics software for correlating genome-wide DNA methylation and gene expression. BMC Genomics, 21:375. https://doi.org/10.1186/s12864-020-6722-x Website
Sheng-Yao Su, I-Hsuan Lu, Wen-Chih Cheng, Wei-Chun Chung, Pao-Yang Chen, Jan-Ming Ho, Shu-Hwa Chen, Chung-Yen Lin (2020) EpiMOLAS: an intuitive web-based framework for genome-wide DNA methylation analysis. BMC Genomics, 21, 163. https://doi.org/10.1186/s12864-019-6404-8 Website
Emilie debladis, Tzuu-Fen Lee, Yan-Jiun Huang, Jui-Hsien Lu, Sandra Mathioni, Marie-Christine Carpentier, Christel Llauro, Davy Pierron, Delphine Mieulet, Emmanuel Guiderdoni, Pao-Yang Chen, Blake Meyers, Olivier Panaud, Eric Lasserre (2020) Construction and characterization of a knock-down RNA interference line of OsNRPD1 in rice (Oryza sativa ssp. Japonica cv. Nipponbare). Philosophical Transactions of the Royal Society B, 375:20190338. https://doi.org/10.1098/rstb.2019.0338
Yang Jie, Lianyu Yuan, Ming‐Ren Yen, Feng Zheng, Rujun Ji, Tao Peng, Dachuan Gu, Songguang Yang, Yuhai Cui, Pao‐Yang Chen, Keqiang Wu, Xuncheng Liu (2019) SWI3B and HDA6 are Required for Transposon Silencing in Arabidopsis The Plant Journal, 102(4), 809-822. https://doi.org/10.1111/tpj.14666
Yi-Jing Lee, Pearl Chang, Jui-Hsien Lu, Pao-Yang Chen*, Chung-Ju Rachel Wang* (2019) Assessing chromatin accessibility in maize using ATAC-seq bioRxiv, https://doi.org/10.1101/526079
You-Yuan Pang, Jui-Hsien Lu, Pao-Yang Chen (2019) Behavioral Epigenetics: Perspectives based on Experience-Dependent Epigenetic Inheritance Epigenomes 3(3), 18. https://doi.org/10.3390/epigenomes3030018
Nien's artwork for cover page : 
Phuong Nguyen Tran, Ming-Ren Yen, Chen-Yu Chiang, Hsiao-Ching Lin*, Pao-Yang Chen* (2019) Detecting and prioritizing biosynthetic gene clusters for bioactive compounds in bacteria and fungi Applied Microbiology and Biotechnology, Vol 103, Issue 8, 3277-3287. https://doi.org/10.3390/epigenomes3030018
Ta-Ching Chen, Pin-Yi She, Dong Feng Chen, Jui-Hsien Lu, Chang-Hao
Yang, Ding-Siang Huang, Pao-Yang Chen, Chen-Yu Lu, Kin-Sang Cho, Hsin-Fu Chen, Wei-Fang Su (2019) Polybenzyl glutamate biocompatible scaffold promotes the efficiency of
retinal differentiation toward retinal ganglion cell lineage from human
induced pluripotent stem cells International Journal of Molecular Sciences, 20(1), 178. https://doi.org/10.3390/ijms20010178
Jie Hou, Xiaowen Shi, Chen Chen, Soliman Islam, Adam F. Johnson, Tatsuo Kanno, Bruno Huettel, Ming-Ren Yen, Fei-Man Hsu, Tieming Ji, Pao-Yang Chen, Marjori Matzke, Antonius J.M. Matzke, Jianlin Cheng, James A. Birchler (2018) Global impacts of chromosomal imbalance on gene expression in Arabidopsis and other taxa. Proceedings of the National Academy of Sciences, 115(48), E11321-E11330. https://doi.org/10.1073/pnas.1807796115 Commentary-Genomic Balance and Speciation
Fei-Man Hsu, Moloya Gohain, Archana Allishe, Yan-Jiun Huang, Jo-Ling Liao, Lin-Yun Kuang and Pao-Yang Chen (2018) Dynamics of the Methylome and Transcriptome during the Regeneration of Rice. Epigenomes, 2(3), 14. https://doi.org/10.3390/epigenomes2030014
Yu Yuan Huang, Yan-Jiun Huang, Pao-Yang Chen (2018) BS-Seeker3: Ultrafast pipeline for bisulfite sequencing. BMC Bioinformatics, 19, 111. https://doi.org/10.3390/epigenomes2030014
Fei-Man Hsu, Chung-Ju Rachel Wang* and Pao-Yang Chen* (2018) Reduced Representation Bisulfite Sequencing in Maize. Bio-protocol, 8(6): e2778. https://doi.org/10.21769/BioProtoc.2778
Pearl Chang, Moloya Gohain, Ming-Ren Yen, Pao-Yang Chen (2018) Computational Methods for Assessing Chromatin Hierarchy. Computational and Structural Biotechnology Journal, 16, 43-53. https://doi.org/10.1016/j.csbj.2018.02.003
Pearl Chang, Yu-Fang Tseng, Pao-Yang Chen* and Chung-Ju Rachel Wang* (2018) Using flow cytometry to isolate maize meiocytes for next generation sequencing: A time and labor efficient method. Current Protocols in Plant Biology, 3(2), e20068. https://doi.org/10.1002/cppb.20068
Yu Tao☨, Ming-Ren Yen☨, Tsotne Chitiashvili, Haruko Nakano, Rachel Kim, Linzi Hosohama, Yao Chang Tan, Atsushi Nakano, Pao-Yang Chen*, Amander T Clark* (2018) TRIM28-regulated transposon repression is required for human germline competency and not primed or naïve human pluripotency. Stem Cell Reports, Volume 10, Issue 1, p243–256. https://doi.org/10.1016/j.stemcr.2017.11.020
. (☨ co-first, * co-corresponding authors)
Fei-Man Hsu, Moloya Gohain, Pearl Chang, Jui-Hsien Lu, Pao-Yang Chen (2018) Bioinformatics of Epigenetic Data Generated from Next-Generation Sequencing. Epigenetics in Human Disease, 2nd edition, Elsevier, Vol.6 in Translational Epigenetics 65-106. https://doi.org/10.1016/B978-0-12-812215-0.00004-2
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Jer-Young Lin, Brandon Le, Min Chen, Kelli F. Henry, Jungim Hur, Tzung-Fu Hsieh, Pao-Yang Chen, Julie M. Pelletier, Matteo Pellegrini, Robert L. Fischer, John J. Harada, Robert B. Goldberg (2017) Similarity between soybean and Arabidopsis seed methylomes and loss of non-CG methylation does not affect seed development. Proceedings of the National Academy of Sciences, 114(45), E9730-E9739. https://doi.org/10.1073/pnas.1716758114
Ming-Ren Yen, Der-Fen Suen, Fei-Man Hsu, Yi-Hsiu Tsai, Hongyong Fu, Wolfgang Schmidt*, and Pao-Yang Chen* (2017) Deubiquitinating enzyme OTU5 contributes to DNA methylation patterns and is critical for phosphate nutrition signals. Plant Physiology, 175(4), 1826-1838. https://doi.org/10.1104/pp.17.01188
Ta-Ching Chen, Chao-Yuan Yeh, Chao-Wen Lin, Chung-May Yang, Chang-Hao Yang, I-Hung Lin, Pao-Yang Chen, Jung-Yu Cheng, Fung-Rong Hu (2017) Vascular hypoperfusion in acute optic neuritis is a potentially new neurovascular model for demyelinating diseases.
PLoS ONE, 12(9), e0184927. https://doi.org/10.1371/journal.pone.0184927
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 and Yu-Ming Ju (2017) A termite symbiotic mushroom maximizing sexual activity at growing tips of vegetative hyphae. Botanical Studies, 58, 1-14. https://doi.org/10.1186/s40529-017-0191-9
Fei-Man Hsu, Ming-Ren Yen, Chi-Ting Wang, Chien-Yu Lin, Chung-Ju Rachel Wang* and Pao-Yang Chen* (2017) Optimized reduced representation bisulfite sequencing reveals tissue-specific mCHH islands in maize. Epigenetics & Chromatin, 10, 1-16. https://doi.org/10.1186/s13072-017-0148-y Gitlab
Pao-Yang Chen☨, Alison Chu☨, Wen-Wei Liao, Liudmilla Rubbi, Carla Janzen, Fei-Man Hsu, Amit Ganguly, Shanthie Thamotharan, Matteo Pelligrini, Sherin Devaskar (2017) Prenatal growth patterns and birthweight are associated with differential DNA methylation and gene expression of cardiometabolic risk genes in human placentas. Reproductive Sciences, 25(4), 523-539. https://doi.org/10.1177/1933719117716779
Meng-Ying Wu, Chia-Yeh Lin, Hsin-Yi Tseng, Fei-Man Hsu, Pao-Yang Chen and Cheng-Fu Kao (2017) H2B ubiquitylation and the histone chaperone Asf1 cooperatively mediate the formation and maintenance of heterochromatin silencing. Nucleic Acids Research, 45(14), 8225-8238. https://doi.org/10.1093/nar/gkx422
Fei-Man Hsu, Pao-Yang Chen (2017) Game theory in epigenetic reprogramming: Comment on: “Epigenetic game theory: How to compute the epigenetic control of maternal-to-zygotic transition” by Qian Wang et al. Physics of Life Reviews, 20, 143-145. https://doi.org/10.1016/j.plrev.2017.01.005.
Sheng-Yao Su, Shu-Hwa Chen, I-Hsuan Lu, Yih-Shien Chiang, Yu-Bin Wang, Pao-Yang Chen* and Chung-Yen Lin* (2016) TEA: the epigenome platform for Arabidopsis methylome study. BMC Genomics, 17, 141-149. https://doi.org/10.1186/s12864-016-3326-6 Website
Joseph Hargan-Calvopina, Sara Taylor, Helene Cook, Zhongxun Hu, Serena A. Lee, Ming-Ren Yen, Yih-Shien Chiang, Pao-Yang Chen, Amander T. Clark (2016) Stage-Specific Demethylation in Primordial Germ Cells Safeguards against Precocious Differentiation. Developmental Cell 39(1), 75-86. https://doi.org/10.1016/j.devcel.2016.07.019
Wai-Shin Yong☨, Fei-Man Hsu☨, Pao-Yang Chen (2016) Profiling genome-wide DNA methylation. Epigenetics & Chromatin, 9, 1-16. https://doi.org/10.1186/s13072-016-0075-3 (1st most cited paper of Epigenetics & Chromatin in 2016)
Colin Flinders☨, Larry Lam☨, Liudmilla Rubbi, Roberto Ferrari, Sorel Fitz-Gibbon, Pao-Yang Chen, Michael Thompson, Heather Christofk, David B Agus, Daniel Ruderman, Parag Mallick and Matteo Pellegrini (2016) Epigenetic changes mediated by polycomb repressive complex 2 and E2a are associated with drug resistance in a mouse model of lymphoma. Genome Medicine, 8, 1-11. https://doi.org/10.1186/s13073-016-0305-0
Fei-Man Hsu☨, Wai-Shin Yong☨, Pao-Yang Chen (2016) Views on Profiling Genomewide DNA Methylation and Crop Methylomes. Crop, Environment & Bioinformatics, 13, 39-51.
https://doi.org/10.30061/CEB.201603_13(1).0004
Fei-Man Hsu, Amander T Clark, Pao-Yang Chen (2015) Epigenetic reprogramming in the mammalian germline.Oncotarget, 6(34), 35151. https://doi.org/10.18632/oncotarget.6206
Wen-Wei Liao☨, Ming-Ren Yen☨, Evaline Ju, Fei-Man Hsu, Larry Lam, Pao-Yang Chen (2015) MethGO: a comprehensive tool for analyzing whole genome bisulte sequencing data.BMC Genomics, 16, 1-8. https://doi.org/10.1186/1471-2164-16-S12-S11 Software
Gkountela, Kelvin Zhang, Tiasha Shaq, Wen-Wei Liao, Joseph Hargan-Calvopina, Pao-Yang Chen*, Amander T Clark* (2015) DNA Demethylation Dynamics in the Human Prenatal Germline. Cell, 161(6), 1425-1436. https://doi.org/10.1016/j.cell.2015.05.012 (co-corresponding authors)
Taku Sasaki, Tatsuo Kanno, Shih-Chieh Liang, Pao-Yang Chen, Wen-Wei Liao, Wen-Dar Lin, Antonius J.M. Matzke* and Marjori Matzke* (2015) An Rtf2 domain-containing protein influences pre-mRNA splicing and is essential for embryonic development in Arabidopsis thaliana. Genetics, 200(2), 523-535. https://doi.org/10.1534/genetics.115.176438
Pao-Yang Chen☨, Barbara Montanini☨, Wen-Wei Liao, Marco Morselli, Artur Jaroszewicz, David Lopez, Simone Ottonello and Matteo Pellegrini (2014) A comprehensive resource of genomic, epigenomic and transcriptomic sequencing data for the black truffe Tuber melanosporum. GigaScience, 3:25. https://doi.org/10.1186/2047-217X-3-25
Barbara Montanini☨, Pao-Yang Chen☨, Marco Morselli, Artur Jaroszewicz, David Lopez, Francis Martin, Simone Ottonello and Matteo Pellegrini. (2014) Non-exhaustive DNA methylation-mediated transposon silencing in the black truffle genome, a complex fungal genome with massive repeat element content. Genome Biology 15, 1-16. https://doi.org/10.1186/s13059-014-0411-5
Negar M Ghahramani, Tuck C Ngun, Pao-Yang Chen, Yuan Tian, Sangitha Krishnan, Stephanie Muir, Liudmilla Rubbi, Arthur P Arnold, Geert J de Vries, Nancy G Forger, Matteo Pellegrini, Eric Vilain (2014) The effects of perinatal testosterone
exposure on the DNA methylome of the mouse brain are late-emerging.Biol Sex Differ, 5, 1-18. https://doi.org/10.1186/2042-6410-5-8
Sasaki T, Lee TF, Liao, Wen-Wei, Naumann U, Liao Joling, Eun CH, Huang YY, Fu JL, Pao-Yang Chen, Meyers BC, Matzke AJM, and Matzke M. (2014) Distinct and concurrent pathways of Pol II and Pol IV-dependent siRNA biogenesis at a repetitive trans-silencer locus in Arabidopsis thaliana.The Plant Journal, 79(1), 127-138. https://doi.org/10.1111/tpj.12545
Guo W, Fiziev P, Yan W, Cokus S, Sun X, Zhang MQ, Pao-Yang Chen* & Pellegrini M.* (2013) BS-Seeker2: a versatile aligning pipeline for bisulfite sequencing data. BMC Genomics, 14(1): 774. https://doi.org/10.1186/1471-2164-14-774 (co-corresponding authors) Github
Pao-Yang Chen, Amit Ganguly, Liudmilla Rubbi, Luz D. Orozco, Marco Morselli, Davin Ashraf, Artur Jaroszewicz, Suhua Feng, Steve E. Jacobsen, Atsushi Nakano, Sherin U. Devaskar, and Matteo Pellegrini (2013) Intra-uterine calorie restriction affects placental DNA methylation and gene expression.Physiol. Genomics, 45(14), 565-576. https://doi.org/10.1152/physiolgenomics.00034.2013
J. Vincent, Y. Huang, Pao-Yang Chen, S. Feng, J.. Calvopia, K. Nee, S. Lee, T. Le, A. Yoon, K. Faull, G. Fan, A. Rao, S. Jacobsen, M. Pellegrini, and A. Clark (2013) Stage-Specific Roles for Tet1 and Tet2 in DNA Demethylation in Primordial Germ Cells. Cell Stem Cell, 12(4):470-8 https://doi.org/10.1016/j.stem.2013.01.016
Pao-Yang Chen, M. Pellegrini (2012) Methylomes, Epigenetic Regulation and Epigenomics from the Encyclopedia of Molecular Cell Biology and Molecular Medicine, pp. 815-837, UK: John Wiley & Sons, Inc. (invited review)
Pao-Yang Chen, S. Feng, J. Joo, S. Jacobsen, M. Pellegrini (2011) A comparative analysis of DNA methylation across human embryonic stem cell lines, Genome Biology 12:R62 (highly accessed)
Shota Atsumi, Tung-Yun Wu, I. Machado, W. Huang, Pao-Yang Chen, Matteo Pellegrini, James C Liao (2010) Evolution, genomic analysis, and reconstruction of isobutanol tolerance in Escherichia coli. Nature-EMBO Molecular Systems Biology 6: 499
R. Chodavarapu, S. Feng, Y. Bernatavichute, Pao-Yang Chen, H. Stroud, Y. Yu, J. Hetzel, F. Kuo, J. Kim, S. Cokus, D. Casero, M. Bernal, P. Huijser, A. Clark, U. Krmer, S. Merchant, X. Zhang, S. Jacobsen, M. Pellegrini (2010) Relationship between nucleosome positioning and DNA methylation. Nature 466, 388-392
S. Feng, S. Cokus, X. Zhang, Pao-Yang Chen, M. Bostick, M. Goll, J. Hetzel, J. Jain, S. Strauss, M. Halpern, C. Ukomadu, K. Sadler, M. Pellegrini, S. Jacobsen (2010) Conservation and divergence of plant and animal methylation patterning. Proceedings of the National Academy of Sciences,
11;107(19):8689-94
Pao-Yang Chen, S. Cokus, M. Pellegrini, (2010) BS Seeker: precise mapping for bisulfite sequencing. BMC Bioinformatics 11: 203 (highly accessed)
R. Hamer*, Pao-Yang Chen*, J. Armitage, G. Reinert, C. Deane (2010) Deciphering chemotaxis pathways using cross species comparisons. BMC Systems Biology, 4: 3 (co-furst authors)
Pao-Yang Chen, C. Deane, G. Reinert (2008) Predicting and validating protein interactions using network structure. PLoS Computational Biology 4(7): e1000118
Pao-Yang Chen, C. Deane, G. Reinert (2007) A statistical approach using network structure in the prediction of protein characteristics. Bioinformatic 23 (17): 2314-2321
C. Lin, S. Chen, C. Cho, C. Chen, F. Lin, C. Lin, Pao-Yang Chen, C. Lo, C. Hsiung, (2006) Fly-DPI: database of protein interactomes for D. melanogaster in the approach of systems biology.BMC Bioinformatics 7 (5) S18
C. Chen, C. Lin, C. Cho, L. Wang, C. Chang, Pao-Yang Chen, C. Lo, C. Hsiung, (2005) HP-DPI: Helicobacter Pylori Database of Protein Interactomes, a combined experimental and inferring interactions. Bioinformatics, 21(7):1288-1290
Y. Chen, J. Chen, K. Richard, Pao-Yang Chen, D. Christiani, (2004) Lung adenocarcinoma and human papillomavirus infection. Cancer15;101(6):1428-36
C. Hwu, C. Hsiao, S. Kuo, K. Wu, C. Ting, T. Quertermous, B, Rodriguez, I. Chen, J. Grove, Pao-Yang Chen, L. Ho, (2004) Physical inactivity is an important lifestyle determinant of insulin resistance in hypertensive patients. Blood Pressure 13 (6): 355-361 (Selected in the Outstanding Thesis Collection by Ministry of National Defense, Taiwan)
Ching Liu and Pao-Yang Chen (1999) Mapping and analysis of Quantitative Trait Loci (QTL) for Poisson distributed data. Chinese Agronomy Journal 9(3):127-141
Epigenetic discrimination of DNA United States Patent Application 16/325097
如何透過DNA的密碼 預測植物改造成功？ 中研院植微所科普專欄 (2023)
基因上的魔法師—不改 DNA 就可以調整性狀的「表觀遺傳調控」，為作物改良帶來新曙光 黃湘芹、謝若微、李映漾、陳柏仰 PanSci 泛科學 (2022)
中研院研究室實習初體驗：做研究要耐得住寂寞？我認為不盡然 吳東憲 The News Lens 關鍵評論網 (2020)
Fei-Man Hsu, Pao-Yang Chen (2017) 表觀遺傳重置 – 胚胎如何抹除父母的記憶並保留細胞的全能性？ 中研院週報知識天地 1604
7分之1機率不孕，下一代更嚴重？5大因素解析 BabyHome編輯 (2016)
不孕症 可能天注定 聯合報 (2015)
中研院跨國研究 助了解不孕症 蘋果日報 (2015)
禍延三代！懷孕初期吸菸、飲酒 恐導致子孫不孕 自由時報 (2015)
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