Academia Sinica Life Science Library -- Publications

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Publications

Inst. of Plant and Microbial Biology - 陳柏仰 Chen, Pao-Yang

Journal 64

Lin PY, Chang YT, Huang YC, Chen PY. Estimating genome-wide DNA methylation heterogeneity with methylation patterns. Epigenetics & chromatin. 16(1), 44, 2023-11-09. [JCR]　[WOS]
Hsieh JA, Chang P, Kuang LY, Hsing YC, Chen PY. Rice transformation treatments leave specific epigenome changes beyond tissue culture. Plant physiology. 2023, doi: 10.1093/plphys/, 2023-07-03. [JCR]　[WOS]
Lee H, Lin PY, Chen PY. There's more to it: uncovering genomewide DNA methylation heterogeneity. Epigenomics. doi: 10.2217/epi-2023-0228, doi: 10.2217/epi-2023-0228, 2023-07-24. [JCR]　[WOS]
Lu RJ, Lin PY, Yen MR, Wu BH, Chen PY. MethylC-analyzer: a comprehensive downstream pipeline for the analysis of genome-wide DNA methylation. Botanical studies. 64(1), 1, 2023-01-06. [JCR]　[WOS]
Liu YW, Fu SH, Chien MW, Hsu CY, Lin MH, Dong JL, Lu RJ, Lee YJ, (Chen PY), Wang CH, Sytwu HK. Blimp-1 molds the epigenetic architecture of IL-21-mediated autoimmune diseases through an autoregulatory circuit. JCI insight. 7(11), e151614, 2022-06-08. [JCR]　[WOS]
Lowe MG, Yen MR, Hsu FM, Hosohama L, Hu Z, Chitiashvili T, Hunt TJ, Gorgy I, Bernard M, Wamaitha SE, (Chen PY)*, Clark AT*. EED is required for mouse primordial germ cell differentiation in the embryonic gonad. Developmental cell. 57(12), 1482-1495.e5, 2022-06-20. [JCR]　[WOS]
Tu YT, Chen CY, Huang YS, Chang CH, Yen MR, Hsieh JA, (Chen PY)*, Wu K*. HISTONE DEACETYLASE 15 and MOS4-Associated Complex subunits 3A/3B coregulate intron retention of ABA-responsive genes. Plant physiology. doi: 10.1093/plphys/kiac271, kiac271, 2022-06-07. [JCR]　[WOS]
Kuo FC*, Huang YC, Yen MR, Lee CH, Hsu KF, Yang HY, Wu LW, Lu CH, Hsu YJ, (Chen PY)*. Aberrant overexpression of HOTAIR inhibits abdominal adipogenesis through remodelling of genome-wide DNA methylation and transcription. Molecular metabolism. 60, 101473, 2022-03-12. [JCR]　[WOS]
Chang YT, Yen MR, (Chen PY)*. BSImp: Imputing Partially Observed Methylation Patterns for Evaluating Methylation Heterogeneity. Frontiers in Bioinformatics. 2, doi: 10.3389/fbinf.2, 2022-02-10. [JCR]　[WOS]
Yang CY, Lu RJ, Lee MK, Hsiao FS, Yen YP, Cheng CC, Hsu PS, Tsai YT, Chen SK, Liu IH, (Chen PY)* and Lin SP*. Transcriptome Analysis of Dnmt3l Knock-Out Mice Derived Multipotent Mesenchymal Stem/Stromal Cells During Osteogenic Differentiation. Frontiers in cell and developmental biology. 9, 615098, 2021-02-25. [JCR]　[WOS]
Lu JH, Liu YT, Huang CW, Yen MR, Lin CY and (Chen PY)*. ATACgraph: profiling genome wide chromatin accessibility from ATAC-seq. FRONTIERS IN GENETICS. 11, 618478, 2021-01-13. [JCR]　[WOS]
Nai YS, Huang YC, Yen MR and (Chen PY)*. Diversity of Fungal DNA Methyltransferases and Their Association With DNA Methylation Patterns. Frontiers in microbiology. 11, 616922, 2021-01-22. [JCR]　[WOS]
Ke HM, Lee HH, Lin CY, Liu YC, Lu MR, Hsieh JW, Chang CC, Wu PH, Lu M, Li JY, Shang G, Lu JH, Nagy LG, (Chen PY), Kao HW and Tsai I*. Mycena genomes resolve the evolution of fungal bioluminescence. Proceedings of the National Academy of Sciences. 117 (49), 31267-31277, 2020-12-08. [JCR]　[WOS]
Hsieh JW, Yen MR and (Chen PY)*. Epigenomic regulation of OTU5 in Arabidopsis thaliana. GENOMICS. 112(5), 3549-3559, 2020-09. [JCR]　[WOS]
Hung FY, Chen C, Yen MR, Hsieh JW, Li CL, Shih YH, Chen FF, (Chen PY)*, Cui YH* and Wu KQ*. The expression of long non-coding RNAs is associated with H3Ac and H3K4me2 changes regulated by the HDA6-LDL1/2 histone modification complex in Arabidopsis. NAR Genomics and Bioinformatics. 2(3), lqaa066, 2020-09-21. [JCR]　[WOS]
Zhu H, (Chen PY), Zhong S, Dardick C, Callahan A, An YQ, Nocker S, Yang YZ, Zhong GY, Abbott A and Liu Z*. Thermal-responsive genetic and epigenetic regulation of DAM cluster controlling dormancy and chilling requirement in peach floral buds. HORTICULTURE RESEARCH. 7, 114, 2020-08-01. [JCR]　[WOS]
Teng CS, Wu BH, Yen MR, (Chen PY)*. MethGET: web-based bioinformatics software for correlating genome-wide DNA methylation and gene expression. BMC genomics. 21(1), 375, 2020-05-29. [JCR]　[WOS]
Su SY, Lu IH, Cheng WC, Chung WC, (Chen PY), Ho JM, Chen SH* and Lin CY*. EpiMOLAS: an intuitive web-based framework for genome-wide DNA methylation analysis. BMC GENOMICS. 21(Suppl 3):163., 2020-04-02. [JCR]　[WOS]
Debladis E, Lee TF, Huang YJ, Lu JH, Mathioni Sandra M., Carpentier M-C, Llauro C, Pierron D, Mieulet D, Guiderdoni E, (Chen PY), Meyers Blake C., Panaud O, Lasserre E. 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: Biological Sciences. 375(1795) 20190338, 2020-03-30. [JCR]　[WOS]
Yang J, Yuan L, Yen MR, Zheng F, Ji R, Peng T, Gu D, Yang S, Cui Y, (Chen PY), Wu K*, Liu X*. SWI3B and HDA6 interact and are required for transposon silencing in Arabidopsis. The Plant journal : for cell and molecular biology. 102(4), 809-822, 2020-01-22. [JCR]　[WOS]
Pang YY, Lu JH, (Chen PY)*. Behavioral Epigenetics: Perspectives Based on Experience-Dependent Epigenetic Inheritance. Epigenomes. 3(3), 18, 2019-09. [JCR]　[WOS]
Tran PN, Yen MR, Chiang CY, Lin HC*, (Chen PY)*. Detecting and prioritizing biosynthetic gene clusters for bioactive compounds in bacteria and fungi. Applied microbiology and biotechnology. 103(8), 3277–3287, 2019-03-12. [JCR]　[WOS]
Chen TC, She PY, Chen DF, Lu JH, Yang CH, Huang DS, (Chen PY), Lu CY, Cho KS, Chen HF, Su WF. 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), 2019-01-05. [JCR]　[WOS]
Hou J, Shi X, Chen C, Islam MS, Johnson AF, Kanno T, Huettel B, Yen MR, Hsu FM, Ji T, (Chen PY), Matzke M, Matzke AJM, Cheng J, Birchler JA. Global impacts of chromosomal imbalance on gene expression in Arabidopsis and other taxa. Proceedings of the National Academy of Sciences of the United States of America. 115(48), E11321-E11330, 2018-11-14. [JCR]　[WOS]
Hsu FM, Gohain M, Allishe A, Huang YJ, Liao JL, Kuang LY, (Chen PY)*. Dynamics of the Methylome and Transcriptome during the Regeneration of Rice. Epigenomes. 2(3), 14, 2018-07-21. [JCR]　[WOS]
Chang P, Tseng YF, (Chen PY)*, Wang CR*. 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, 2018-05-24. [JCR]　[WOS]
Huang KYY, Huang YJ, (Chen PY)*. BS-Seeker3: ultrafast pipeline for bisulfite sequencing. BMC bioinformatics. 19(1), 111, 2018-04-03. [JCR]　[WOS]
Hsu FM, Wang CJR*, (Chen PY)*. Reduced Representation Bisulfite Sequencing in Maize Bio-protocol. Bio-protocol. 8(6), e2778, 2018-03-20. [JCR]　[WOS]
Chang P, Gohain M, Yen MR, (Chen PY)*. Computational Methods for Assessing Chromatin Hierarchy. Computational and structural biotechnology journal. 16, 43-53, 2018-02-15. [JCR]　[WOS]
Yen MR, Suen DF, Hsu FM, Tsai YH, Fu H, Schmidt W*, (Chen PY)*. Deubiquitinating Enzyme OTU5 Contributes to DNA Methylation Patterns and Is Critical for Phosphate Nutrition Signals. Plant physiology. 175(4), 1826-1838, 2017-12. [JCR]　[WOS]
Tao Y, Yen MR, Chitiashvili T, Nakano H, Kim R, Hosohama L, Tan YC, Nakano A, (Chen PY)*, Clark AT*. TRIM28-Regulated Transposon Repression Is Required for Human Germline Competency and Not Primed or Naive Human Pluripotency. STEM CELL REPORTS. 10(1), 243-256, 2017-12-28. [JCR]　[WOS]
Lin JY, Le BH, Chen M, Henry KF, Hur J, Hsieh TF, (Chen PY), Pelletier JM, Pellegrini M, Fischer RL, Harada JJ, Goldberg RB. 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 of the United States of America. 114(45), E9730-E9739, 2017-10-23. [JCR]　[WOS]
Hsieh HM, Chung MC, (Chen PY), Hsu FM, Liao WW, Sung AN, Lin CR, Wang CR, Kao YH, Fang MJ, Lai CY, Huang CC, Chou JC, Chou WN, Chang BC, Ju YM*. A termite symbiotic mushroom maximizing sexual activity at growing tips of vegetative hyphae. Botanical studies. 58(1), 39, 2017-09-19. [JCR]　[WOS]
Chen TC, Yeh CY, Lin CW, Yang CM, Yang CH, Lin IH, (Chen PY), Cheng JY, Hu FR. Vascular hypoperfusion in acute optic neuritis is a potentially new neurovascular model for demyelinating diseases. PloS one. 12(9), e0184927, 2017-09-19. [JCR]　[WOS]
Wu MY, Lin CY, Tseng HY, Hsu FM, (Chen PY), Kao CF*. H2B ubiquitylation and the histone chaperone Asf1 cooperatively mediate the formation and maintenance of heterochromatin silencing. Nucleic acids research. 45(14), 8225-8238, 2017-08-21. [JCR]　[WOS]
Hsu FM, Yen MR, Wang CT, Lin CY, Wang CR*, (Chen PY)*. Optimized reduced representation bisulfite sequencing reveals tissue-specific mCHH islands in maize. Epigenetics & chromatin. 10(1), 42, 2017-08-30. [JCR]　[WOS]
(Chen PY), Chu A, Liao WW, Rubbi L, Janzen C, Hsu FM, Thamotharan S, Ganguly A, Lam L, Montoya D, Pellegrini M, Devaskar SU*. Prenatal Growth Patterns and Birthweight Are Associated With Differential DNA Methylation and Gene Expression of Cardiometabolic Risk Genes in Human Placentas: A Discovery-Based Approach. Reproductive sciences (Thousand Oaks, Calif.). 25(4), 523-539, 2017-04. [JCR]　[WOS]
Hsu FM, (Chen PY)*. 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, 2017-03. [JCR]　[WOS]
Su SY, Chen SH, Lu IH, Chiang YS, Wang YB, (Chen PY)*, Lin CY*. TEA: the epigenome platform for Arabidopsis methylome study. BMC genomics. 17(Suppl 13), 1027, 2016-12-22. [JCR]　[WOS]
Hargan-Calvopina J, Taylor S, Cook H, Hu Z, Lee SA, Yen MR, Chiang YS, (Chen PY), Clark AT*. Stage-Specific Demethylation in Primordial Germ Cells Safeguards against Precocious Differentiation. Developmental cell. 39(1), 75-86, 2016-09-08. [JCR]　[WOS]
Yong WS, Hsu FM, (Chen PY)*. Profiling genome-wide DNA methylation. Epigenetics & Chromatin. 9, 26, 2016-06-29. [JCR]　[WOS]
Flinders C, Lam L, Rubbi L, Ferrari R, Fitz-Gibbon S, (Chen PY), Thompson M, Christofk H, B Agus D, Ruderman D, Mallick P*, Pellegrini M*. 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), 54, 2016-05-04. [JCR]　[WOS]
Hsu FM, Yong WS, (Chen PY)*. Views on Profiling Genomewide DNA Methylation and Crop Methylomes. Crop, Environment & Bioinformatics. 13, 39-51, 2016-03-01. [JCR]　[WOS]
Liao WW, Yen MR, Ju E, Hsu FM, Lam L, (Chen PY)*. MethGo: a comprehensive tool for analyzing whole-genome bisulfite sequencing data. BMC genomics. 16 Suppl 12, S11, 2015-12-09. [JCR]　[WOS]
Hsu FM, Clark A, (Chen PY)*. Epigenetic reprogramming in the mammalian germline. Oncotarget. 6(34), 35151-35152, 2015-10-21. [JCR]　[WOS]
Sasaki T, Kanno T, Liang SC, (Chen PY), Liao WW, Lin WD, Matzke AJ*, Matzke M*. An Rtf2 Domain-Containing Protein Influences Pre-mRNA Splicing and Is Essential for Embryonic Development in Arabidopsis thaliana. Genetics. 200(2), 523-535, 2015-06-01. [JCR]　[WOS]
Gkountela S, Zhang KX, Shafiq TA, Liao WW, Hargan-Calvopina J, (Chen PY)*, Clark AT*. DNA Demethylation Dynamics in the Human Prenatal Germline. Cell. 161(6), 1425-36, 2015-05-21. [JCR]　[WOS]
(Chen PY), Montanini B, Liao WW, Morselli M, Jaroszewicz A, Lopez D, Ottonello S*, Pellegrini M*. A comprehensive resource of genomic, epigenomic and transcriptomic sequencing data for the black truffle Tuber melanosporum. GigaScience. 3, 25, 2014-10-30. [JCR]　[WOS]
Montanini B, (Chen PY), Morselli M, Jaroszewicz A, Lopez D, Martin F, Ottonello S*, Pellegrini M*. Non-exhaustive DNA methylation-mediated transposon silencing in the black truffle genome, a complex fungal genome with massive repeat element content. Genome biology. 15(7), 411, 2014-07-31. [JCR]　[WOS]
Ghahramani NM, Ngun TC, (Chen PY), Tian Y, Krishnan S, Muir S, Rubbi L, Arnold AP, de Vries GJ, Forger NG, Pellegrini M, Vilain E*. The effects of perinatal testosterone exposure on the DNA methylome of the mouse brain are late-emerging. Biology of sex differences. 5, 8, 2014-06-13. [JCR]　[WOS]
Sasaki T, Lee TF, Liao WW, Naumann U, Liao JL, Eun C, Huang YY, Fu JL, (Chen PY), Meyers BC, Matzke AJ, Matzke M*. 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 : for cell and molecular biology. 79(1), 127-38, 2014-05-05. [JCR]　[WOS]
Guo W, Fiziev P, Yan W, Cokus S, Sun X, Zhang MQ, (Chen PY)*, Pellegrini M*. BS-Seeker2: a versatile aligning pipeline for bisulfite sequencing data. BMC genomics. 14, 774, 2013-11-10. [JCR]　[WOS]
Vincent JJ, Huang Y, (Chen PY), Feng S, Calvopina JH, Nee K, Lee SA, Le T, Yoon AJ, Faull K, Fan G, Rao A, Jacobsen SE, Pellegrini M, Clark AT. Stage-specific roles for tet1 and tet2 in DNA demethylation in primordial germ cells. Cell stem cell. 12(4), 470-8, 2013-04-04. [JCR]　[WOS]
(Chen PY), Ganguly A, Rubbi L, Orozco LD, Morselli M, Ashraf D, Jaroszewicz A, Feng S, Jacobsen SE, Nakano A, Devaskar SU, Pellegrini M. Intrauterine calorie restriction affects placental DNA methylation and gene expression. Physiological genomics. 45(14), 565-76, 2013. [JCR]　[WOS]
Feng S, Cokus SJ, Zhang X, (Chen PY), Bostick M, Goll MG, Hetzel J, Jain J, Strauss SH, Halpern ME, Ukomadu C, Sadler KC, Pradhan S, Pellegrini M, Jacobsen SE. Conservation and divergence of methylation patterning in plants and animals. Proceedings of the National Academy of Sciences of the United States of America. 107(19), 8689-8694, 2010. [JCR]　[WOS]
Hamer R, (Chen PY), Armitage JP, Reinert G, Deane CM. Deciphering chemotaxis pathways using cross species comparisons. BMC systems biology. 4, 3, 2010. [JCR]　[WOS]
Atsumi S, Wu TY, Machado IM, Huang WC, (Chen PY), Pellegrini M, Liao JC. Evolution, genomic analysis, and reconstruction of isobutanol tolerance in Escherichia coli. Molecular systems biology. 6, 449, 2010. [JCR]　[WOS]
Chodavarapu RK, Feng S, Bernatavichute YV, (Chen PY), Stroud H, Yu Y, Hetzel JA, Kuo F, Kim J, Cokus SJ, Casero D, Bernal M, Huijser P, Clark AT, Kramer U, Merchant SS, Zhang X, Jacobsen SE, Pellegrini M. Relationship between nucleosome positioning and DNA methylation. Nature. 466(7304), 388-392, 2010. [JCR]　[WOS]
(Chen PY)*, Deane CM, Reinert G. Predicting and validating protein interactions using network structure. PLoS computational biology. 4(7), e1000118, 2008. [JCR]　[WOS]
(Chen PY)*, Deane CM, Reinert G. A statistical approach using network structure in the prediction of protein characteristics. BIOINFORMATICS. 23(17), 2314-2321, 2007. [JCR]　[WOS]
Lin CY, Chen SH, Cho CS, Chen CL, Lin FK, Lin CH, (Chen PY), Lo CZ, Hsiung CA. Fly-DPI: database of protein interactomes for D. melanogaster in the approach of systems biology. BMC bioinformatics. 7 Suppl 5, S18, 2006. [JCR]　[WOS]
Lin CY, Chen CL, Cho CS, Wang LM, Chang CM, (Chen PY), Lo CZ, Hsiung CA. hp-DPI: Helicobacter pylori database of protein interactomes--embracing experimental and inferred interactions. BIOINFORMATICS. 21(7), 1288-1290, 2005. [JCR]　[WOS]
Chen YC, Chen JH, Richard K, (Chen PY), Christiani DC. Lung adenocarcinorna and human papillomavirus infection. Cancer. 101(6), 1428-1436, 2004. [JCR]　[WOS]
Hwu CM, Hsiao CF, Kuo SW, Wu KD, Ting CT, Quertermous T, Rodriguez B, Chen I, Grove J, (Chen PY), Hoo LT. Physical inactivity is an important lifestyle determinant of insulin resistance in hypertensive patients. Blood pressure. 13(6), 355-361, 2004. [JCR]　[WOS]

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