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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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2023 Journal Article Repressive epigenetic mechanisms, such as the H3K27me3 histone modification, were predicted to affect muscle gene expression and its mineral content in Nelore cattleAfonso, Juliana, Shim, Woo Jun, Boden, Mikael, Salinas Fortes, Marina Rufino, da Silva Diniz, Wellison Jarles, de Lima, Andressa Oliveira, Rocha, Marina Ibelli Pereira, Cardoso, Tainã Figueiredo, Bruscadin, Jennifer Jessica, Gromboni, Caio Fernando, Nogueira, Ana Rita Araujo, Mourão, Gerson Barreto, Zerlotini, Adhemar, Coutinho, Luiz Lehmann and de Almeida Regitano, Luciana Correia (2023). Repressive epigenetic mechanisms, such as the H3K27me3 histone modification, were predicted to affect muscle gene expression and its mineral content in Nelore cattle. Biochemistry and Biophysics Reports, 33 101420, 1-9. doi: 10.1016/j.bbrep.2023.101420 |
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2023 Journal Article PDGF-AB Reduces Myofibroblast Differentiation Without Increasing Proliferation After Myocardial InfarctionHume, Robert D., Deshmukh, Tejas, Doan, Tram, Shim, Woo Jun, Kanagalingam, Shaan, Tallapragada, Vikram, Rashid, Fairooj, Marcuello, Maria, Blessing, Daniel, Selvakumar, Dinesh, Raguram, Kalyan, Pathan, Faraz, Graham, Dinny, Ounzain, Samir, Kizana, Eddy, Harvey, Richard P., Palpant, Nathan J. and Chong, James J.H. (2023). PDGF-AB Reduces Myofibroblast Differentiation Without Increasing Proliferation After Myocardial Infarction. JACC: Basic to Translational Science, 8 (6), 658-674. doi: 10.1016/j.jacbts.2022.11.006 |
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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 |
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2022 Journal Article 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. Journal of Molecular and Cellular Cardiology, 173, S182-S182. doi: 10.1016/j.yjmcc.2022.08.344 |
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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 |
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2021 Journal Article Elp2 mutations perturb the epitranscriptome and lead to a complex neurodevelopmental phenotypeKojic, Marija, Gawda, Tomasz, Gaik, Monika, Begg, Alexander, Salerno-Kochan, Anna, Kurniawan, Nyoman D., Jones, Alun, Drożdżyk, Katarzyna, Kościelniak, Anna, Chramiec-Głąbik, Andrzej, Hediyeh-Zadeh, Soroor, Kasherman, Maria, Shim, Woo Jun, Sinniah, Enakshi, Genovesi, Laura A., Abrahamsen, Rannvá K., Fenger, Christina D., Madsen, Camilla G., Cohen, Julie S., Fatemi, Ali, Stark, Zornitza, Lunke, Sebastian, Lee, Joy, Hansen, Jonas K., Boxill, Martin F., Keren, Boris, Marey, Isabelle, Saenz, Margarita S., Brown, Kathleen ... Wainwright, Brandon J. (2021). Elp2 mutations perturb the epitranscriptome and lead to a complex neurodevelopmental phenotype. Nature Communications, 12 (1) 2678, 2678. doi: 10.1038/s41467-021-22888-5 |
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2021 Journal Article J-domain proteins promote client relay from Hsp70 during tail-anchored membrane protein targetingCho, Hyunju, Shim, Woo Jun, Liu, Yumeng and Shan, Shu-ou (2021). J-domain proteins promote client relay from Hsp70 during tail-anchored membrane protein targeting. Journal of Biological Chemistry, 296 100546, 1-15. doi: 10.1016/j.jbc.2021.100546 |
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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 |
