Publications

Results 1-49 of 49 (Search time: 0.005 seconds).

Issue DateTitleAuthor(s)RelationscopusWOSFulltext/Archive link
12024Bioinformatics Analysis of DNA MethylationLin, PY; Chen, KL; Lin, GJ; Huang, SC; Chen, PY Methods in Molecular Biology (Springer Nature)
22024Whole Genome Bisulfite SequencingHsu, FM; Chen, PY ; Pellegrini, MMethods in Molecular Biology (Springer Nature)
32024Chapter 3 - Bioinformatics of epigenetic data generated from next-generation sequencingSheu, CY L; Huang, YC; Lin, PY; Lin, GJ; Chen, PY Epigenetics in Human Disease (Third Edition) (United Kingdom : Elsevier)
42023Epigenomic Footprints in the Regeneration and Transformation of RiceHsieh, JW A; Chang, P; Kuang, LY; Hsing, YI, C; Chen, PY 
52023Rice Transformation Leaves Footprints on the Genome-Wide DNA Methylation LandscapeChen, PY 
62023Estimating genome-wide DNA methylation heterogeneity with methylation patternsLin, PY; Chang, YT; Huang, YC; Chen, PY Epigenetics & chromatin 16(1), 44
72023Estimating Genome-Wide DNA Methylation Heterogeneity in RiceLin, PY; Chang, YT; Lee, J; Huang, YCand, Chen, PY 
82023There's more to it: uncovering genomewide DNA methylation heterogeneityLee, H; Lin, PY; Chen, PY Epigenomics 15(13), 687-691
92023Rice transformation treatments leave specific epigenome changes beyond tissue cultureHsieh, JA; Chang, P; Kuang, LY ; Hsing, YC ; Chen, PY Plant physiology 193(2), 1297-1312
102023Detecting the Interplay Between DNA Methylation and Lipid Production in PlantsHsieh, JW; Liu, YC; Huang, LT; Nakamura, Y; Chen, PY 
112023Methylome Imputation by Methylation PatternsChang, YS; Yen, MR; Chen, PY Methods in molecular biology (Clifton, N.J.) (New York, USA : Humana)
122023MethylC-analyzer: a comprehensive downstream pipeline for the analysis of genome-wide DNA methylationLu, RJ; Lin, PY; Yen, MR; Wu, BH; Chen, PY Botanical studies 64(1), 1
132022Epigenome Bioinformatics in PlantsChen, PY 
142022Epigenome bioinformatics in rice and plantsChen, PY 
152022EED is required for mouse primordial germ cell differentiation in the embryonic gonadLowe, MG; Yen, MR; Hsu, FM; Hosohama, L; Hu, Z; Chitiashvili, T; Hunt, TJ; Gorgy, I; Bernard, M; Wamaitha, SE; Chen, PY ; Clark, ATDevelopmental cell 57(12), 1482-1495.e5
162022HISTONE DEACETYLASE 15 and MOS4-associated complex subunits 3A/3B coregulate intron retention of ABA-responsive genesTu, YT; Chen, CY; Huang, YS; Chang, CH; Yen, MR; Hsieh, JA; Chen, PY ; Wu, KPlant physiology 190(1), 882-897
172022Blimp-1 molds the epigenetic architecture of IL-21–mediated autoimmune diseases through an autoregulatory circuitLiu, YW; Fu, SH; Chien, MW; Hsu, CY; Lin, MH; Dong, JL; Lu, RJ; Lee, YJ; Chen, PY ; Wang, CH; Sytwu, HKJCI insight 7(11), e151614
182022Aberrant overexpression of HOTAIR inhibits abdominal adipogenesis through remodelling of genome-wide DNA methylation and transcriptionKuo, FC; Huang, YC; Yen, MR; Lee, CH; Hsu, KF; Yang, HY; Wu, LW; Lu, CH; Hsu, YJ; Chen, PY Molecular metabolism 60, 101473
192022BSImp: Imputing Partially Observed Methylation Patterns for Evaluating Methylation HeterogeneityChang, YT; Yen, MR; Chen, PY Frontiers in Bioinformatics 2, 815289
202021Dissecting the Dynamic Changes of Methylome During Rice TransformationChen, PY 
212021Transcriptome Analysis of Dnmt3l Knock-Out Mice Derived Multipotent Mesenchymal Stem/Stromal Cells During Osteogenic DifferentiationYang, CY; Lu, RJ; Lee, MK; Hsiao, FS; Yen, YP; Cheng, CC; Hsu, PS; Tsai, YT; Chen, SK; Liu, IH; Chen, PY ; Lin, SPFrontiers in cell and developmental biology 9, 615098
222021Diversity of Fungal DNA Methyltransferases and Their Association With DNA Methylation PatternsNai, YS; Huang, YC; Yen, MR; Chen, PY Frontiers in microbiology 11, 616922
232021ATACgraph: Profiling Genome-Wide Chromatin Accessibility From ATAC-seqRita Jui-Hsein Lu; Yen-Ting Liu; Chih Wei Huang; Ming-Ren Yen; Chung-Yen Lin ; Pao-Yang Chen FRONTIERS IN GENETICS 11, 618478
242020Mycena genomes resolve the evolution of fungal bioluminescenceKe, Huei-Mien; Lee, Hsin-Han; Lin, Chan-Yi Ivy; Liu, Yu-Ching; Lu, Min R.; Hsieh, Jo-Wei Allison; Chang, Chiung-Chih; Wu, Pei-Hsuan; Lu, Meiyeh Jade ; Li, Jeng-Yi; Shang, Gaus; Lu, Rita Jui-Hsien; Nagy, László G.; Chen, Pao-Yang ; Kao, Hsiao-Wei; Tsai, Isheng Jason Proceedings of the National Academy of Sciences 117(49), 31267-31277
252020The expression of long non-coding RNAs is associated with H3Ac and H3K4me2 changes regulated by the HDA6-LDL1/2 histone modification complex in ArabidopsisHung, FY; Chen, C; Yen, MR; Hsieh, JW; Li, CL; Shih, YH; Chen, FF; Chen, PY ; Cui, YH; Wu, KQNAR Genomics and Bioinformatics 2(3), lqaa066
262020Epigenomic regulation of OTU5 in Arabidopsis thalianaHsieh, JW; Yen, MR; Chen, PY GENOMICS 112(5), 3549-3559
272020Thermal-responsive genetic and epigenetic regulation of DAM cluster controlling dormancy and chilling requirement in peach floral budsZhu, H; Chen, PY ; Zhong, S; Dardick, C; Callahan, A; An, YQ; Nocker, S; Yang, YZ; Zhong, GY; Abbott, A; Liu, ZHORTICULTURE RESEARCH 7, 114
282020MethGET: web-based bioinformatics software for correlating genome-wide DNA methylation and gene expressionTeng, CS; Wu, BH; Yen, MR; Chen, PY BMC GENOMICS 21, 375
292020EpiMOLAS: an intuitive web-based framework for genome-wide DNA methylation analysisSheng-Yao Su; I-Hsuan Lu; Wen-Chih Cheng; Wei-Chun Chung; Pao-Yang Chen ; Jan-Ming Ho ; Shu-Hwa Chen; Chung-Yen Lin BMC Genomics 21, 163
302020Construction 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, EricPhilosophical Transactions of the Royal Society B: Biological Sciences 375(1795), 20190338
312019SWI3B and HDA6 interact and are required for transposon silencing in ArabidopsisYang, Jie; Yuan, Lianyu; Yen, Ming‐Ren; Zheng, Feng; Ji, Rujun; Peng, Tao; Gu, Dachuan; Yang, Songguang; Cui, Yuhai; Chen, Pao-Yang ; Wu, Keqiang; Liu, XunchengThe Plant Journal Early View
322019The change of genome-wide DNA methylation during rice transformationChen, PY 
332019Investigation of Genome-wide DNA Methylation in Plants, Animals and FungiChen, PY 
342019Exploring the transcriptome-methylome dynamics in Termitomyces eurhizusHuang, YC; Hsieh, HM; Lin, CY; Ju, YM; Chen, PY 
352019Behavioral Epigenetics: Perspectives Based on Experience-Dependent Epigenetic InheritancePang, YY; Lu, JH; Chen, PY Epigenomes 3(3), 18
362019The transformation impact on methylome and transcriptome of transgenic riceGohain, M; Chang, P; Lu, JH; Hsu, FM; Kuang, LY; Hsing, YI; Chen, PY 
372019Detecting 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
382019Polybenzyl glutamate biocompatible scaffold promotes the efficiency of retinal differentiation toward retinal ganglion cell lineage from human-induced pluripotent stem cellsTa-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 SuInternational Journal of Molecular Sciences 20(1), 178
392018Exploring the transcriptome-methylome dynamics in Termitomyces mushroomHsu, FM; Hsieh, HM; Lu, JH; Hsieh, CJ; Huang, YJ; Yen, MR; Lin, CY; Ju, YM; Chen, PY 
402017Deubiquitinating 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
412017Similarity between soybean and Arabidopsis seed methylomes and loss of non-CG methylation does not affect seed development.Lin, JY ; Le, BH; Chen, M; Henry, KF; Hur, J; Hsieh, TF; Chen, PY ; Pelletier, JM; Pellegrini, M; Fischer, RL; Harada, JJ; Goldberg, RBProceedings of the National Academy of Sciences of the United States of America 114(45), E9730-E9739
422017Vascular hypoperfusion in acute optic neuritis is a potentially new neurovascular model for demyelinating diseases.Chen, TC; Yeh, CY; Lin, CW; Yang, CM; Yang, CH; Lin, IH; Chen, PY ; Cheng, JY; Hu, FRPloS one 12(9), e0184927
432017A termite symbiotic mushroom maximizing sexual activity at growing tips of vegetative hyphaeHuei-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
442017Optimized reduced representation bisulfite sequencing reveals tissue-specific mCHH islands in maize.Hsu, FM; Yen, MR; Wang, CT; Lin, CY; Wang, CJR ; Chen, PY Epigenetics & chromatin 10, 42
452017H2B ubiquitylation and the histone chaperone Asf1 cooperatively mediate the formation and maintenance of heterochromatin silencing.Wu, MY; Lin, CY; Tseng, HY; Hsu, FM; Chen, PY ; Kao, CFNucleic acids research 45(14), 8225-8238
462017Game 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.Hsu, FM; Chen, PY Physics of life reviews 20, 143-145
472014Distinct 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, MThe Plant journal : for cell and molecular biology 79(1), 127-38
482014The effects of perinatal testosterone exposure on the DNA methylome of the mouse brain are late-emerging.Ghahramani, NM; Ngun, TC; Chen, PY ; Tian, Y; Krishnan, S; Muir, S; Rubbi, L; Arnold, AP; de Vries, GJ; Forger, NG; Pellegrini, M; Vilain, EBiology of sex differences 5, 8
492013BS-Seeker2: a versatile aligning pipeline for bisulfite sequencing data.Guo, W; Fiziev, P; Yan, W; Cokus, S; Sun, X; Zhang, MQ; Chen, PY ; Pellegrini, MBMC genomics 14, 774