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2026 Journal Article Glycaemic variability underlies myocyte dysfunction and myocardial injury risk in diabetesCao, Yuanzhao, Redd, Meredith A., Outhwaite, Jennifer E., Mizikovsky, Dalia, Shim, Woo Jun, Fang, Chen, Vedelago, Courtney, Tan, Clarissa, Wu, Zhixuan, Daygon, Dara, Stark, Terra, Palfreyman, Robin, Chiu, Han Sheng, Thomas, Ulrich, Dragicevic, Elena, Sng, Julian D. J., Saez, Natalie J., Barrett, Helen L., Dorey, Emily S., King, Glenn F., Wuethrich, Alain, Trau, Matt, Shah, Sonia, Short, Kirsty R. and Palpant, Nathan J. (2026). Glycaemic variability underlies myocyte dysfunction and myocardial injury risk in diabetes. Nature Communications, 17 (1) 5612, 1. doi: 10.1038/s41467-026-71809-x |
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2026 Journal Article A scalable, multi-resolution consensus clustering approach for prioritizing robust signals from high-throughput screensBao, Shaine Chenxin, Pishas, Kathleen I., Cowley, Karla J., Zhao, Qiongyi, Goodall, Emily C. A., Henderson, Ian R., Liu, Xin, Marinovic, Evanny, Carey, Mark S., Campbell, Ian G., Simpson, Kaylene J., Cheasley, Dane, Mizikovsky, Dalia and Palpant, Nathan J. (2026). A scalable, multi-resolution consensus clustering approach for prioritizing robust signals from high-throughput screens. Briefings in Bioinformatics, 27 (3) bbag242. doi: 10.1093/bib/bbag242 |
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Featured 2025 Journal Article Conserved facultative heterochromatin across cell types identify regulatory sequences underpinning cell identity and diseaseSinniah, Enakshi, Mizikovsky, Dalia, Shim, Woo Jun, Chow, Chris Siu Yeung, Souilmi, Yassine, Cheng, Fei-Fei, Zeng, Zhili, Laurie, Jordan, Foster, Matthew, Shah, Sonia, Bodén, Mikael, Zeng, Jian, Llamas, Bastien and Palpant, Nathan J. (2025). Conserved facultative heterochromatin across cell types identify regulatory sequences underpinning cell identity and disease. Nucleic Acids Research, 53 (20) gkaf971, 1-23. doi: 10.1093/nar/gkaf971 |
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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 |
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2024 Journal Article Acid-sensing ion channel 1a blockade reduces myocardial injury in rodent models of myocardial infarctionRedd, Meredith A, Yoshikawa, Yusuke, Khan, Nemat, Waqar, Maleeha, Saez, Natalie J, Outhwaite, Jennifer E, Russell, Jake S, Hanna, Amy D, Chiu, Han S, Er, Sing Yan, Butcher, Neville J, Mardon, Karine, Fraser, John F, Smythe, Mark L, Rash, Lachlan D, Thomas, Walter G, King, Glenn F, Reichelt, Melissa E and Palpant, Nathan J (2024). Acid-sensing ion channel 1a blockade reduces myocardial injury in rodent models of myocardial infarction. European Heart Journal, 45 (17), 1571-1574. doi: 10.1093/eurheartj/ehad793 |
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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 |
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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 |
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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 |
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2022 Journal Article Organization of gene programs revealed by unsupervised analysis of diverse gene–trait associationsMizikovsky, Dalia, Naval Sanchez, Marina, Nefzger, Christian M, Cuellar Partida, Gabriel and Palpant, Nathan J (2022). Organization of gene programs revealed by unsupervised analysis of diverse gene–trait associations. Nucleic Acids Research, 50 (15) e87, 1-12. doi: 10.1093/nar/gkac413 |
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2021 Journal Article Therapeutic inhibition of acid sensing ion channel 1a recovers heart function after ischemia-reperfusion injury (vol 144, pg 947, 2021)Redd, 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, Xia, 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 (vol 144, pg 947, 2021). Circulation, 144 (12), E211-E211. doi: 10.1161/CIR.0000000000001020 |
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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 |
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2018 Journal Article Single-cell transcriptomic analysis of cardiac differentiation from human PSCs reveals HOPX-dependent cardiomyocyte maturationFriedman, Clayton E., Nguyen, Quan, Lukowski, Samuel W., Helfer, Abbigail, Chiu, Han Sheng, Miklas, Jason, Levy, Shiri, Suo, Shengbao, Han, Jing-Dong Jackie, Osteil, Pierre, Peng, Guangdun, Jing, Naihe, Baillie, Greg J., Senabouth, Anne, Christ, Angelika N., Bruxner, Timothy J., Murry, Charles E., Wong, Emily S., Ding, Jun, Wang, Yuliang, Hudson, James, Ruohola-Baker, Hannele, Bar-Joseph, Ziv, Tam, Patrick P.L., Powell, Joseph E. and Palpant, Nathan J. (2018). Single-cell transcriptomic analysis of cardiac differentiation from human PSCs reveals HOPX-dependent cardiomyocyte maturation. Cell Stem Cell, 23 (4), 586-598. doi: 10.1016/j.stem.2018.09.009 |
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2026 Journal Article TRIAGE Toolkit: Streamlined Discovery of Regulatory Genes and ElementsZhao, Qiongyi, Shen, Sophie, Sun, Yuliangzi, Sinniah, Enakshi, Boden, Mikael, Palpant, Nathan J. and Shim, Woo Jun (2026). TRIAGE Toolkit: Streamlined Discovery of Regulatory Genes and Elements. Current Protocols, 6 (7) e70413, e70413-7. doi: 10.1002/cpz1.70413 |
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2026 Journal Article Computational modelling of cell identityShim, Woo Jun, Chow, Chris Siu Yeung, Bao, Shaine Chenxin, Zhao, Qiongyi and Palpant, Nathan J. (2026). Computational modelling of cell identity. Biochemical Journal, 483 (6), 1049-1071. doi: 10.1042/bcj20250132 |
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2026 Journal Article Identifying therapeutic targets in low‐grade serous ovarian carcinomas with no specific molecular profilePishas, Kathleen I, Cowley, Karla J, Marinovic, Evanny, Köbel, Martin, Llaurado‐Fernandez, Marta, Kim, Hannah, Bao, Shaine Chenxin, Mizikovsky, Dalia, Palpant, Nathan J, Shrestha, Raunak, Vary, Robert, Luu, Jennii, Meunier, Liliane, Semple, Timothy, Blancafort, Pilar, Golden, Emily, Cohen, Paul A, Carey, Mark S, Campbell, Ian G, Simpson, Kaylene J and Cheasley, Dane (2026). Identifying therapeutic targets in low‐grade serous ovarian carcinomas with no specific molecular profile. The Journal of Pathology, 269 (4-5) path.70075, 446-461. doi: 10.1002/path.70075 |
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2026 Journal Article Preparing healthcare providers to use polygenic risk scores: a qualitative study of learning needs and educational preferencesClark, Amy, Wallingford, Courtney K., McInerney-Leo, Aideen, Berkman, Jennifer, Nisselle, Amy, Terrill, Bronwyn, Palpant, Nathan, Young, Mary-Anne, James, Paul A. and Yanes, Tatiane (2026). Preparing healthcare providers to use polygenic risk scores: a qualitative study of learning needs and educational preferences. BMJ Open, 16 (5) e111898, 1-10. doi: 10.1136/bmjopen-2025-111898 |
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2026 Other Outputs Protocol-dependent cardiomyocyte states determine disease modelling capacity of human iPSCsShen, Sophie, Tan, Clarissa, Cao, Yuanzhao, Chow, Chris Siu Yeung, Mizikovsky, Dalia, Reid, Janice, Dingwall, Steve, Prowse, Andrew, Sun, Yuliangzi, Wu, Zhixuan, Negi, Sumedha, Bao, Shaine Chenxin, Sinniah, Enakshi, Shim, Woo Jun, Zhao, Qiongyi, Thorpe, Jordan, Zahabi, Azadeh, Hanna, Amy, Cheng, Trishia, Hill, Adam, Hudson, James, Chong, James J. H. and Palpant, Nathan J. (2026). Protocol-dependent cardiomyocyte states determine disease modelling capacity of human iPSCs. doi: 10.64898/2026.03.29.715135 |
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2026 Other Outputs Hierarchical control of cardiomyocyte maturation and ischaemia sensitivity by metabolic culture conditionsCao, Yuanzhao, Chow, Chris Siu Yeung, Negi, Sumedha, Shim, Woo Jun, Shen, Sophie, Fang, Chen and Palpant, Nathan J. (2026). Hierarchical control of cardiomyocyte maturation and ischaemia sensitivity by metabolic culture conditions. doi: 10.64898/2026.03.12.711459 |
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2026 Journal Article Bacterial reporter–paired scRNA sequencing reveals cross talk between zinc starvation and zinc toxicity in macrophage antibacterial defensevon Pein, Jessica B., Andersen, Stacey B., Xu, Jon, Phan, Minh-Duy, Dalton, Emma K., Koczerka, Michael, Stocks, Claudia J., Curson, James E. B., Vandeleur, Zoe, Condon, Nicholas D., Hancock, Steven J., Nefzger, Christian M., Palpant, Nathan J., Ramnath, Divya, Kapetanovic, Ronan, Schembri, Mark A. and Sweet, Matthew J. (2026). Bacterial reporter–paired scRNA sequencing reveals cross talk between zinc starvation and zinc toxicity in macrophage antibacterial defense. Proceedings of the National Academy of Sciences, 123 (11) e2530503123, 1-12. doi: 10.1073/pnas.2530503123 |
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2026 Journal Article The changing landscape of gene expression analysisZhao, Qiongyi, Shen, Sophie, Shim, Woo Jun and Palpant, Nathan J. (2026). The changing landscape of gene expression analysis. Briefings in Bioinformatics, 27 (2) bbag185, 2. doi: 10.1093/bib/bbag185 |
