Publications

2026

Fei-Man Hsu☨, Jo-Wei Allison Hsieh☨, Shiang-Chin Huang, Pao-Yang Chen*. DNA methylation dynamics in rice regeneration and transformation. The International Symposium on Rice Functional Genomics 2024 (Open Access Book). 2026. Accepted January 13, 2026.

2025

Sissy E. Wamaitha, Ernesto J. Rojas, Francesco Monticolo, Fei-Man Hsu, Enrique Sosa, Amanda M. Mackie, Kiana Oyama, Maggie Custer, Melinda Murphy, Diana J. Laird, Jian She, Jon D. Hennebold, and Amander T. Clark. Defining the cell and molecular origins of the primate ovarian reserve. Nature Communications. 6, 7539, 2025.

Fei-Man Hsu, Matteo Pellegrini, and Pao-Yang Chen. Library preparation for genome-wide DNA methylation profiling. Bio-protocol, 15(21), 2025.

Enrique Sosa, Sissy E. Wamaitha, Fei-Man Hsu, Mary Jasmine D. Lara, Kiana Oyama, Maggie Custer, Melinda Murphy, Jon D. Hennebold, Young Sun Hwang, and Amander T. Clark. Testicular somatic and germ cell maturation during rhesus macaque development. Proceedings of the National Academy of Sciences of the United States of America, 122(26):e2419995122, 2025.

Fei-Man Hsu, Harry C. Pickering, Liudmilla Rubbi, Michael Thompson, Elaine F. Reed, Matteo Pellegrini, and Joanna M. Schaenman. DNA methylation predicts infection risk in kidney transplant recipients. Life Science Alliance, 8(7):e202403124, 2025.

We showed that peripheral blood DNA methylation profiles predict which kidney transplant recipients will develop infections. We built machine-learning models from genome-wide methylation data to generate epigenetic biomarkers for infection risk stratification.

Fei-Man Hsu, Harry Pickering, Monica Cappelletti, Elaine Reed, Matteo Pellegrini, and Joanna M. Schaenman. T cell subtypes and DNA methylome dynamics predict infection after kidney transplantation. Open Forum Infectious Diseases, 12(Suppl 5), 2025.

We showed that shifts in T cell subtype composition and DNA methylation over time precede infection after kidney transplantation. We integrated immune cell deconvolution with longitudinal methylome analysis to identify predictive immune-epigenetic signatures.

2024

Fei-Man Hsu, Rashmi P. Mohanty, Liudmilla Rubbi, Michael Thompson, Harry Pickering, Elaine F. Reed, John R. Greenland, Joanna M. Schaenman, and Matteo Pellegrini. An epigenetic human cytomegalovirus infection score predicts viremia risk in seropositive lung transplant recipients. Epigenetics, 19(1):2408843, 2024.

Using genome-wide DNA methylation data and bioinformatic modeling, we developed an epigenetic score to predict CMV viremia risk in seropositive lung transplant recipients, a group lacking reliable predictors.

Fei-Man Hsu and Paul Horton. MethylSeqLogo: DNA methylation smart sequence logos. BMC Bioinformatics, 25(Suppl 2):326, 2024. Gitlab

MethylSeqLogo is able to visualize DNA methylation directly within sequence motifs. It extends sequence logo models to incorporate methylation information, revealing methylation-dependent motif patterns missed by standard approaches.

2023

Enrique Sosa, Sinthia Kabir Mumu, Christian C. Alvarado, Qiu Ya Wu, Isaias Roberson, Alejandro Espinoza, Fei-Man Hsu, Kaori Saito, Timothy J. Hunt, Jared E. Faith, Matthew G. Lowe, Jonathan A. DiRusso, and Amander T. Clark. Reconstituted ovaries self-assemble without an ovarian surface epithelium. Stem Cell Reports, 18:1–13, 2023.

Fei-Man Hsu, Qiu Ya Wu, Emily B. Fabyanic, Alex Wei, Hao Wu, and Amander T. Clark. TET1 facilitates specification of early human lineages including germ cells. iScience, 26(7):107191, 2023.

We showed that the DNA demethylation enzyme TET1 is required for specification of early human lineages, including primordial germ cells. Genome-wide methylome and transcriptome analyses identified TET1-dependent epigenetic and gene regulatory programs underlying early lineage specification.

2022

Erica C. Pandolfi, Fei-Man Hsu, Mark Duhon, Yi Zheng, Sierra Goldsmith, Jianping Fu, Sherman J. Silber, and Amander T. Clark. In vitro germ cell induction from fertile and infertile monozygotic twin research participants. Cell Reports Medicine, 3(10):100782, 2022.

Matthew G. Lowe, Ming-Ren Yen, Fei-Man Hsu, Linzi Hosohama, Zhongxun Hu, Tsotne Chitiashvili, Timothy J. Hunt, Isaac Gorgy, Matthew Bernard, Sissy E. Wamaitha, Pao-Yang Chen, and Amander T. Clark. EED is required for mouse primordial germ cell differentiation in the embryonic gonad. Developmental Cell, 57(12):1482–1495.e5, 2022.

We showed that the Polycomb regulator EED is required for mouse primordial germ cell differentiation. Genome-wide epigenomic and transcriptomic analyses defined the regulatory programs controlled by Polycomb repression during germ cell development.

Tsotne Chitiashvili, Fei-Man Hsu, Iris Dror, Kathrin Plath, and Amander T. Clark. FGFR3 is expressed by human primordial germ cells and is repressed after meiotic initiation to form primordial oocytes. Stem Cell Reports, 17(6):1268–1278, 2022.

We identified FGFR3 as a marker of human primordial germ cells and showed that it is repressed after meiotic initiation during primordial oocyte formation. Single-cell transcriptomic analysis defined gene expression dynamics during early human germ cell development.

Xinyu Xiang, Yu Tao, Jonathan DiRusso, Fei-Man Hsu, Jinchun Zhang, Ziwei Xue, Julien Pontis, Didier Trono, Wanlu Liu, and Amander T. Clark. Human reproduction is regulated by retrotransposons derived from ancient Hominidae-specific viral infections. Nature Communications, 13(1):463, 2022.

Chiao-Ping Chen, Sheridan Ke-Wing Fok, Cheng-Yi Chen, Fei-Man Hsu, Yu-Wen Hsieh, and Jiun-Hong Chen. Studying Annelida regeneration in a novel model organism: The freshwater Aeolosoma viride. Methods in Molecular Biology, 2450:179–194, 2022.

2020

Tsotne Chitiashvili, Iris Dror, Rachel Kim, Fei-Man Hsu, Rohan Chaudhari, Erica Pandolfi, Di Chen, Simone Liebscher, Katja Schenke-Layland, Kathrin Plath, and Amander T. Clark. Female human primordial germ cells display X-chromosome dosage compensation despite the absence of X-inactivation. Nature Cell Biology, 22(12):1436–1446, 2020.

We answered how female human primordial germ cells balance X-chromosome gene dosage without classical X-inactivation. Single-cell transcriptomics revealed a distinct mechanism of X-chromosome dosage compensation during human germ cell development.

Chiao-Ping Chen, Sheridan Ke-Wing Fok, Yu-Wen Hsieh, Cheng-Yi Chen, Fei-Man Hsu, Yao-Hsiang Chang, and Jiun-Hong Chen. General characterization of regeneration in Aeolosoma viride. Invertebrate Biology, 139(1), 2020.

Before 2020

Marcela K. Tello-Ruiz, Cristina F. Marco, Fei-Man Hsu, Rajdeep S. Khangura, Pengfei Qiao, Sirjan Sapkota, Michelle C. Stitzer, Rachael Wasikowski, Hao Wu, Junpeng Zhan, Kapeel Chougule, Lindsay C. Barone, Cornel Ghiban, Demitri Muna, Andrew C. Olson, Liya Wang, Doreen Ware, and David A. Micklos. Double triage to identify poorly annotated genes in maize: The missing link in community curation. PLOS ONE, 14(10):e0224086, 2019.

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, and James A. Birchler. Global impacts of chromosomal imbalance on gene expression in Arabidopsis and other taxa. Proceedings of the National Academy of Sciences, 115(48):E11321–E11330, 2018. Commentary in Genomic Balance and Speciation

We addressed how chromosomal imbalance globally alters gene expression across the genome. Comparative transcriptomic analyses across species revealed conserved regulatory effects of aneuploidy.

Fei-Man Hsu, Moloya Gohain, Archana Allishe, Yan-Jiun Huang, Jo-Ling Liao, Lin-Yun Kuang, and Pao-Yang Chen. Dynamics of the methylome and transcriptome during the regeneration of rice. Epigenomes, 2(3):14, 2018.

We investigated how epigenetic regulation changes during plant regeneration. Integrated genome-wide methylome and transcriptome analyses revealed dynamic DNA methylation reprogramming associated with regeneration.

Fei-Man Hsu, Chung-Ju Rachel Wang, and Pao-Yang Chen. Reduced representation bisulfite sequencing in maize. Bio-protocol, 8(6):e2778, 2018.

Fei-Man Hsu, Moloya Gohain, Pearl Chang, Jui-Hsien Lu, and Pao-Yang Chen. Bioinformatics of epigenetic data generated from next-generation sequencing. In Epigenetics in Human Disease (2nd ed.). Elsevier, 2018.

Pao-Yang Chen, Alison Chu, Wen-Wei Liao, Fei-Man Hsu, Carla Janzen, Matteo Pellegrini, and Sherin U. Devaskar. 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, Apr;25(4):523-539, 2018

Ming-Ren Yen, Der-Fen Suen, Fei-Man Hsu, Yi-Hsiu Tsai, Hongyong Fu, Wolfgang Schmidt, and Pao-Yang Chen. Deubiquitinating enzyme OTU5 contributes to DNA methylation patterns and is critical for phosphate nutrition signals. Plant Physiology, 175(4):1826–1838, 2017.

Huei-Mei Hsieh, Mei-Chu Chung, Pao-Yang Chen, Fei-Man Hsu, Wen-Wei Liao, Ai-Ning Sung, Chun-Ru Lin, Chung-Ju Rachel Wang, Yu-Hsin Kao, Mei-Jane Fang, Chi-Yung Lai, Chieh-Chen Huang, Jyh-Ching Chou, Wen-Neng Chou, Chia-Han Bill Chang, and Yu-Ming Ju. A termite symbiotic mushroom maximizing sexual activity at growing tips of vegetative hyphae. Botanical Studies, 58(1):39, 2017.

Fei-Man Hsu, Ming-Ren Yen, Chi-Ting Wang, Chien-Yu Lin, Chung-Ju Rachel Wang, and Pao-Yang Chen. Optimized reduced representation bisulfite sequencing reveals tissue-specific mCHH islands in maize. Epigenetics & Chromatin, 10(1):42, 2017.

Fei-Man Hsu and Pao-Yang Chen. Game theory in epigenetic reprogramming: Comment on “Epigenetic game theory: How to compute the epigenetic control of maternal-to-zygotic transition.” Physics of Life Reviews, 20:143–145, 2017.

Meng-Ying Wu, Chia-Yeh Lin, Hsin-Yi Tseng, Fei-Man Hsu, Pao-Yang Chen, and Cheng-Fu Kao. H2B ubiquitylation and the histone chaperone Asf1 cooperatively mediate the formation and maintenance of heterochromatin silencing. Nucleic Acids Research, 45(14):8225–8238, 2017.

Fei-Man Hsu*, Wai-Shin Yong*, and Pao-Yang Chen. Views on profiling genome-wide DNA methylation and crop methylomes. Crop, Environment & Bioinformatics, 13:39–51, 2016.

Wai-Shin Yong*, Fei-Man Hsu*, and Pao-Yang Chen. Profiling genome-wide DNA methylation. Epigenetics & Chromatin, 9:26, 2016.

We clarified how genome-wide DNA methylation can be accurately measured using next-generation sequencing approaches. This highly cited paper established widely used experimental and computational frameworks for methylation profiling.

Fei-Man Hsu, Amander T. Clark, and Pao-Yang Chen. Epigenetic reprogramming in the mammalian germline. Oncotarget, 6(34):35151–35152, 2015.

Wen-Wei Liao, Ming-Ren Yen, Evaline Ju, Fei-Man Hsu, Larry Lam, and Pao-Yang Chen. MethGO: a comprehensive tool for analyzing whole-genome bisulfite sequencing data. BMC Genomics, 16(Suppl 12):S11, 2015.

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