|
2025 Journal Article Progressive fibrosis in human MASLD is associated with spatially linked transcriptomic signatures of metabolic reprogramming and senescenceVu, Hani, Sun, Yuliangzi, Xiong, Zherui, Tan, Xiao, Radford-Smith, Daniel, Causer, Andrew, Dickens, Alex M., Hyötyläinen, Tuulia, Evstafev, Ilia, Oresic, Matej, Nefzger, Christian, O’Sullivan, Eoin D., Watt, Matthew J., Ramm, Grant A., Clouston, Andrew, Irvine, Katharine, Nguyen, Quan H. and Powell, Elizabeth E. (2025). Progressive fibrosis in human MASLD is associated with spatially linked transcriptomic signatures of metabolic reprogramming and senescence. JHEP Reports 101657, 101657. doi: 10.1016/j.jhepr.2025.101657 |
|
2025 Other Outputs Spatial Transcriptomic Signature of Progressive Fibrosis in Human MASLD: Role of Senescence and Metabolic ReprogrammingVu, Hani, Sun, Yuliangzi, Xiong, Zherui, Tan, Xiao, Irvine, Katharine, Nguyen, Quan H. and Powell, Elizabeth E. (2025). Spatial Transcriptomic Signature of Progressive Fibrosis in Human MASLD: Role of Senescence and Metabolic Reprogramming. The University of Queensland. (Dataset) doi: 10.48610/e95155f |
|
2025 Journal Article Atlas of multilineage stem cell differentiation reveals TMEM88 as a developmental regulator of blood pressureShen, Sophie, Werner, Tessa, Lukowski, Samuel W., Andersen, Stacey, Sun, Yuliangzi, Shim, Woo Jun, Mizikovsky, Dalia, Kobayashi, Sakurako, Outhwaite, Jennifer, Chiu, Han Sheng, Chen, Xiaoli, Chapman, Gavin, Martin, Ella M. M. A., Xia, Di, Pham, Duy, Su, Zezhuo, Kim, Daniel, Yang, Pengyi, Tan, Men Chee, Sinniah, Enakshi, Zhao, Qiongyi, Negi, Sumedha, Redd, Meredith A., Powell, Joseph E., Dunwoodie, Sally L., Tam, Patrick P. L., Bodén, Mikael, Ho, Joshua W. K., Nguyen, Quan and Palpant, Nathan J. (2025). Atlas of multilineage stem cell differentiation reveals TMEM88 as a developmental regulator of blood pressure. Nature Communications, 16 (1) 1356, 1-19. doi: 10.1038/s41467-025-56533-2 |
|
2025 Journal Article TRIAGE: an R package for regulatory gene analysisZhao, Qiongyi, Shim, Woo Jun, Sun, Yuliangzi, Sinniah, Enakshi, Shen, Sophie, Boden, Mikael and Palpant, Nathan J. (2025). TRIAGE: an R package for regulatory gene analysis. Briefings in Bioinformatics, 26 (1) bbaf004, 1-13. doi: 10.1093/bib/bbaf004 |
|
2024 Other Outputs Using signatures of cell identity to improve cell type prediction in single cell analysis pipelinesSun, Yuliangzi (2024). Using signatures of cell identity to improve cell type prediction in single cell analysis pipelines. PhD Thesis, Institute for Molecular Bioscience, The University of Queensland. doi: 10.14264/3419a40 |
|
2024 Journal Article Wnt dose escalation during the exit from pluripotency identifies tranilast as a regulator of cardiac mesodermWu, Zhixuan, Shen, Sophie, Mizikovsky, Dalia, Cao, Yuanzhao, Naval-Sanchez, Marina, Tan, Siew Zhuan, Alvarez, Yanina D., Sun, Yuliangzi, Chen, Xiaoli, Zhao, Qiongyi, Kim, Daniel, Yang, Pengyi, Hill, Timothy A., Jones, Alun, Fairlie, David P., Pébay, Alice, Hewitt, Alex W., Tam, Patrick P.L., White, Melanie D., Nefzger, Christian M. and Palpant, Nathan J. (2024). Wnt dose escalation during the exit from pluripotency identifies tranilast as a regulator of cardiac mesoderm. Developmental Cell, 59 (6), 705-722.e8. doi: 10.1016/j.devcel.2024.01.019 |
|
2024 Journal Article HOPX-associated molecular programs control cardiomyocyte cell states underpinning cardiac structure and functionFriedman, Clayton E., Cheetham, Seth W., Negi, Sumedha, Mills, Richard J., Ogawa, Masahito, Redd, Meredith A., Chiu, Han Sheng, Shen, Sophie, Sun, Yuliangzi, Mizikovsky, Dalia, Bouveret, Romaric, Chen, Xiaoli, Voges, Holly K., Paterson, Scott, De Angelis, Jessica E., Andersen, Stacey B., Cao, Yuanzhao, Wu, Yang, Jafrani, Yohaann M.A., Yoon, Sohye, Faulkner, Geoffrey J., Smith, Kelly A., Porrello, Enzo, Harvey, Richard P., Hogan, Benjamin M., Nguyen, Quan, Zeng, Jian, Kikuchi, Kazu, Hudson, James E. and Palpant, Nathan J. (2024). HOPX-associated molecular programs control cardiomyocyte cell states underpinning cardiac structure and function. Developmental Cell, 59 (1), 91-107.e6. doi: 10.1016/j.devcel.2023.11.012 |
|
2023 Journal Article Inferring cell diversity in single cell data using consortium-scale epigenetic data as a biological anchor for cell identitySun, Yuliangzi, Shim, Woo Jun, Shen, Sophie, Sinniah, Enakshi, Pham, Duy, Su, Zezhuo, Mizikovsky, Dalia, White, Melanie D., Ho, Joshua W. K., Nguyen, Quan, Bodén, Mikael and Palpant, Nathan J (2023). Inferring cell diversity in single cell data using consortium-scale epigenetic data as a biological anchor for cell identity. Nucleic Acids Research, 51 (11), e62-e62. doi: 10.1093/nar/gkad307 |
|
2023 Journal Article A transposable element into the human long noncoding RNA CARMEN is a switch for cardiac precursor cell specificationPlaisance, Isabelle, Chouvardas, Panagiotis, Sun, Yuliangzi, Nemir, Mohamed, Aghagolzadeh, Parisa, Aminfar, Farhang, Shen, Sophie, Shim, Woo Jun, Rochais, Francesca, Johnson, Rory, Palpant, Nathan and Pedrazzini, Thierry (2023). A transposable element into the human long noncoding RNA CARMEN is a switch for cardiac precursor cell specification. Cardiovascular Research, 119 (6), 1361-1376. doi: 10.1093/cvr/cvac191 |
|
2022 Conference Publication Alternative splicing of a transposable element into the human long noncoding RNA CARMEN is a switch for cardiac precursor cell specificationPlaisance, Isabelle, Chouvardas, Panagiotis, Sun, Yuliangzi, Nemir, Mohamed, Aghagolzadeh, Parisa, Aminfar, Farhang, Shen, Sophie, Shim, Woo Jun, Rochais, Francesca, Johnson, Rory and Pedrazzini, Thierry (2022). Alternative splicing of a transposable element into the human long noncoding RNA CARMEN is a switch for cardiac precursor cell specification. XXIV World Congress of the International Society for Heart Research, Berlin, Germany, 12–15 June 2022. London, United Kingdom: Academic Press. doi: 10.1016/j.yjmcc.2022.08.344 |
|
2022 Journal Article Defining the Fetal Gene Program at Single-Cell Resolution in Pediatric Dilated CardiomyopathyMehdiabadi, Neda R., Boon Sim, Choon, Phipson, Belinda, Kalathur, Ravi K.R., Sun, Yuliangzi, Vivien, Celine J., ter Huurne, Menno, Piers, Adam T., Hudson, James E., Oshlack, Alicia, Weintraub, Robert G., Konstantinov, Igor E., Palpant, Nathan J., Elliott, David A. and Porrello, Enzo R. (2022). Defining the Fetal Gene Program at Single-Cell Resolution in Pediatric Dilated Cardiomyopathy. Circulation, 146 (14), 1105-1108. doi: 10.1161/circulationaha.121.057763 |
|
2022 Book Chapter Analysing genetic programs of cell differentiation to study cardiac cell diversificationWu, Zhixuan, Shen, Sophie, Sun, Yuliangzi, Werner, Tessa, Bradford, Stephen T. and Palpant, Nathan J. (2022). Analysing genetic programs of cell differentiation to study cardiac cell diversification. Advanced technologies in cardiovascular bioengineering. (pp. 125-167) edited by Jianyi Zhang and Vahid Serpooshan. Cham, Switzerland: Springer International Publishing. doi: 10.1007/978-3-030-86140-7_8 |
|
2021 Journal Article Integrating single-cell genomics pipelines to discover mechanisms of stem cell differentiationShen, Sophie, Sun, Yuliangzi, Matsumoto, Maika, Shim, Woo Jun, Sinniah, Enakshi, Wilson, Sean B., Werner, Tessa, Wu, Zhixuan, Bradford, Stephen T., Hudson, James, Little, Melissa H., Powell, Joseph, Nguyen, Quan and Palpant, Nathan J. (2021). Integrating single-cell genomics pipelines to discover mechanisms of stem cell differentiation. Trends in Molecular Medicine, 27 (12), 1135-1158. doi: 10.1016/j.molmed.2021.09.006 |
|
2021 Journal Article Therapeutic inhibition of acid sensing ion channel 1a recovers heart function after ischemia-reperfusion injuryRedd, Meredith A., Scheuer, Sarah E., Saez, Natalie J., Yoshikawa, Yusuke, Chiu, Han Sheng, Gao, Ling, Hicks, Mark, Villanueva, Jeanette E., Joshi, Yashutosh, Chow, Chun Yuen, Cuellar-Partida, Gabriel, Peart, Jason N., See Hoe, Louise E., Chen, Xiaoli, Sun, Yuliangzi, Suen, Jacky Y., Hatch, Robert J., Rollo, Ben, Xiao, Di, Alzubaidi, Mubarak A.H., Maljevic, Snezana, Quaife-Ryan, Gregory A., Hudson, James E., Porrello, Enzo R., White, Melanie Y., Cordwell, Stuart J., Fraser, John F., Petrou, Steven, Reichelt, Melissa E. ... Palpant, Nathan J. (2021). Therapeutic inhibition of acid sensing ion channel 1a recovers heart function after ischemia-reperfusion injury. Circulation, 144 (12), 947-960. doi: 10.1161/circulationaha.121.054360 |
|
2020 Journal Article Conserved epigenetic regulatory logic infers genes governing cell identityShim, Woo Jun, Sinniah, Enakshi, Xu, Jun, Vitrinel, Burcu, Alexanian, Michael, Andreoletti, Gaia, Shen, Sophie, Sun, Yuliangzi, Balderson, Brad, Boix, Carles, Peng, Guangdun, Jing, Naihe, Wang, Yuliang, Kellis, Manolis, Tam, Patrick P L, Smith, Aaron, Piper, Michael, Christiaen, Lionel, Nguyen, Quan, Bodén, Mikael and Palpant, Nathan J. (2020). Conserved epigenetic regulatory logic infers genes governing cell identity. Cell Systems, 11 (6), 625-639.e13. doi: 10.1016/j.cels.2020.11.001 |
