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2021 Journal Article Long-read cDNA sequencing identifies functional pseudogenes in the human transcriptomeTroskie, Robin-Lee, Jafrani, Yohaann, Mercer, Tim R., Ewing, Adam D., Faulkner, Geoffrey J. and Cheetham, Seth W. (2021). Long-read cDNA sequencing identifies functional pseudogenes in the human transcriptome. Genome Biology, 22 (1) 146, 1-15. doi: 10.1186/s13059-021-02369-0 |
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2020 Journal Article Nanopore sequencing enables comprehensive transposable element epigenomic profilingEwing, Adam D., Smits, Nathan, Sanchez-Luque, Francisco J., Faivre, Jamila, Brennan, Paul M., Richardson, Sandra R., Cheetham, Seth W. and Faulkner, Geoffrey J. (2020). Nanopore sequencing enables comprehensive transposable element epigenomic profiling. Molecular Cell, 80 (5), 915-928.e5. doi: 10.1016/j.molcel.2020.10.024 |
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2020 Journal Article Overcoming challenges and dogmas to understand the functions of pseudogenesCheetham, Seth W., Faulkner, Geoffrey J. and Dinger, Marcel E. (2020). Overcoming challenges and dogmas to understand the functions of pseudogenes. Nature Reviews Genetics, 21 (3), 191-201. doi: 10.1038/s41576-019-0196-1 |
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Featured 2017 Journal Article RNA-DamID reveals cell-type-specific binding of roX RNAs at chromatin-entry sitesCheetham, Seth W and Brand, Andrea H (2017). RNA-DamID reveals cell-type-specific binding of roX RNAs at chromatin-entry sites. Nature structural & molecular biology, 25 (1), 109-114. doi: 10.1038/s41594-017-0006-4 |
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2025 Journal Article Targeted mRNA delivery with bispecific antibodies that tether LNPs to cell-surface markersDietmair, Bettina, Humphries, James, Mercer, Timothy R., Thurecht, Kristofer J., Howard, Christopher B. and Cheetham, Seth W. (2025). Targeted mRNA delivery with bispecific antibodies that tether LNPs to cell-surface markers. Molecular Therapy Nucleic Acids, 36 (2) 102520, 1-7. doi: 10.1016/j.omtn.2025.102520 |
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2025 Journal Article Enhancement of anti-sarcoma immunity by NK cells engineered with mRNA for expression of a EphA2-targeted CARLam, Pui Yeng, Omer, Natacha, Wong, Josh K. M., Tu, Cui, Alim, Louisa, Rossi, Gustavo R., Victorova, Maria, Tompkins, Hannah, Lin, Cheng-Yu, Mehdi, Ahmed M., Choo, Amos, Elliott, Melissa R., Coleborn, Elaina, Sun, Jane, Mercer, Timothy, Vittorio, Orazio, Dobson, Lachlan J., Mclellan, Alexander D., Brooks, Andrew, Tuong, Zewen Kelvin, Cheetham, Seth W., Nicholls, Wayne and Souza-Fonseca-Guimaraes, Fernando (2025). Enhancement of anti-sarcoma immunity by NK cells engineered with mRNA for expression of a EphA2-targeted CAR. Clinical and Translational Medicine, 15 (1) e70140, 1-21. doi: 10.1002/ctm2.70140 |
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2024 Journal Article A scalable, spin‐free approach to generate enhanced induced pluripotent stem cell–derived natural killer cells for cancer immunotherapyRossi, Gustavo R., Sun, Jane, Lin, Cheng‐Yu, Wong, Joshua K.M., Alim, Louisa, Lam, Pui Yeng, Khosrotehrani, Kiarash, Wolvetang, Ernst, Cheetham, Seth W., Derrick, Emily B., Amoako, Akwasi, Lehner, Christoph, Brooks, Andrew J., Beavis, Paul A. and Souza‐Fonseca‐Guimaraes, Fernando (2024). A scalable, spin‐free approach to generate enhanced induced pluripotent stem cell–derived natural killer cells for cancer immunotherapy. Immunology & Cell Biology, 102 (10), 1-11. doi: 10.1111/imcb.12820 |
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2024 Journal Article The activity of early-life gene regulatory elements is hijacked in aging through pervasive AP-1-linked chromatin openingPatrick, Ralph, Naval-Sanchez, Marina, Deshpande, Nikita, Huang, Yifei, Zhang, Jingyu, Chen, Xiaoli, Yang, Ying, Tiwari, Kanupriya, Esmaeili, Mohammadhossein, Tran, Minh, Mohamed, Amin R., Wang, Binxu, Xia, Di, Ma, Jun, Bayliss, Jacqueline, Wong, Kahlia, Hun, Michael L., Sun, Xuan, Cao, Benjamin, Cottle, Denny L., Catterall, Tara, Barzilai-Tutsch, Hila, Troskie, Robin-Lee, Chen, Zhian, Wise, Andrea F., Saini, Sheetal, Soe, Ye Mon, Kumari, Snehlata, Sweet, Matthew J. ... Nefzger, Christian M. (2024). The activity of early-life gene regulatory elements is hijacked in aging through pervasive AP-1-linked chromatin opening. Cell Metabolism, 36 (8), 1858-1881.e23. doi: 10.1016/j.cmet.2024.06.006 |
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2023 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. (2023). HOPX-associated molecular programs control cardiomyocyte cell states underpinning cardiac structure and function. Developmental Cell, 59 (1), 91-107.e1. doi: 10.1016/j.devcel.2023.11.012 |
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2023 Journal Article Vasculature organotropism in drug deliveryAmruta, A., Iannotta, Dalila, Cheetham, Seth W., Lammers, Twan and Wolfram, Joy (2023). Vasculature organotropism in drug delivery. Advanced Drug Delivery Reviews, 201 115054, 1-13. doi: 10.1016/j.addr.2023.115054 |
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2023 Journal Article mRNA vaccine quality analysis using RNA sequencingGunter, Helen M., Idrisoglu, Senel, Singh, Swati, Han, Dae Jong, Ariens, Emily, Peters, Jonathan R., Wong, Ted, Cheetham, Seth W., Xu, Jun, Rai, Subash Kumar, Feldman, Robert, Herbert, Andy, Marcellin, Esteban, Tropee, Romain, Munro, Trent and Mercer, Tim R. (2023). mRNA vaccine quality analysis using RNA sequencing. Nature Communications, 14 (1) 5663, 1-12. doi: 10.1038/s41467-023-41354-y |
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Featured 2022 Journal Article Somatic retrotransposition in the developing rhesus macaque brainBillon, Victor, Sanchez-Luque, Francisco J, Rasmussen, Jay, Bodea, Gabriela O, Gerhardt, Daniel J, Gerdes, Patricia, Cheetham, Seth W, Schauer, Stephanie N, Ajjikuttira, Prabha, Meyer, Thomas J, Layman, Cora E, Nevonen, Kimberly A, Jansz, Natasha, Garcia-Perez, Jose L, Richardson, Sandra R, Ewing, Adam D, Carbone, Lucia and Faulkner, Geoffrey J (2022). Somatic retrotransposition in the developing rhesus macaque brain. Genome Research, 32 (7), gr.276451.121-1314. doi: 10.1101/gr.276451.121 |
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2022 Journal Article Methylartist: tools for visualizing modified bases from nanopore sequence dataCheetham, Seth W., Kindlova, Michaela and Ewing, Adam D. (2022). Methylartist: tools for visualizing modified bases from nanopore sequence data. Bioinformatics, 38 (11), 3109-3112. doi: 10.1093/bioinformatics/btac292 |
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2022 Journal Article Reduced chromatin accessibility correlates with resistance to Notch activationvan den Ameele, Jelle, Krautz, Robert, Cheetham, Seth W., Donovan, Alex P. A., Llorà-Batlle, Oriol, Yakob, Rebecca and Brand, Andrea H. (2022). Reduced chromatin accessibility correlates with resistance to Notch activation. Nature Communications, 13 (1) 2210, 2210. doi: 10.1038/s41467-022-29834-z |
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2021 Journal Article In vivo targeted DamID identifies CHD8 genomic targets in fetal mouse brainWade, A. Ayanna, van den Ameele, Jelle, Cheetham, Seth W., Yakob, Rebecca, Brand, Andrea H. and Nord, Alex S. (2021). In vivo targeted DamID identifies CHD8 genomic targets in fetal mouse brain. iScience, 24 (11) 103234, 103234. doi: 10.1016/j.isci.2021.103234 |
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2021 Journal Article Processed pseudogenes: a substrate for evolutionary innovation. Retrotransposition contributes to genome evolution by propagating pseudogene sequences with rich regulatory potential throughout the genomeTroskie, Robin-Lee, Faulkner, Geoffrey J. and Cheetham, Seth W. (2021). Processed pseudogenes: a substrate for evolutionary innovation. Retrotransposition contributes to genome evolution by propagating pseudogene sequences with rich regulatory potential throughout the genome. BioEssays, 43 (11) 2100186, 2100186. doi: 10.1002/bies.202100186 |
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2021 Journal Article Microdeletion of 9q22.3: a patient with minimal deletion size associated with a severe phenotypeEwing, Adam D., Cheetham, Seth W., McGill, James J., Sharkey, Michael, Walker, Rick, West, Jennifer A., West, Malcolm J. and Summers, Kim M. (2021). Microdeletion of 9q22.3: a patient with minimal deletion size associated with a severe phenotype. American Journal of Medical Genetics Part A, 185 (7) ajmg.a.62224, 2070-2083. doi: 10.1002/ajmg.a.62224 |
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2020 Book Chapter Mapping RNA-Chromatin interactions in vivo with RNA-DamIDCheetham, Seth W. and Brand, Andrea H. (2020). Mapping RNA-Chromatin interactions in vivo with RNA-DamID. RNA-Chromatin Interactions. (pp. 255-264) edited by Ulf Andersson Vang Ørom. New York, NY, United States: Humana Press. doi: 10.1007/978-1-0716-0680-3_18 |
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2019 Journal Article LINE-1 Evasion of epigenetic repression in humansSanchez-Luque, Francisco J., Kempen, Marie-Jeanne H.C., Gerdes, Patricia, Vargas-Landin, Dulce B., Richardson, Sandra R., Troskie, Robin-Lee, Jesuadian, J. Samuel, Cheetham, Seth W., Carreira, Patricia E., Salvador-Palomeque, Carmen, García-Cañadas, Marta, Muñoz-Lopez, Martin, Sanchez, Laura, Lundberg, Mischa, Macia, Angela, Heras, Sara R., Brennan, Paul M., Lister, Ryan, Garcia-Perez, Jose L., Ewing, Adam D. and Faulkner, Geoffrey J. (2019). LINE-1 Evasion of epigenetic repression in humans. Molecular Cell, 75 (3), 590-604.e12. doi: 10.1016/j.molcel.2019.05.024 |
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2019 Journal Article DamID as a versatile tool for understanding gene regulationAughey, Gabriel N., Cheetham, Seth W. and Southall, Tony D. (2019). DamID as a versatile tool for understanding gene regulation. Development, 146 (6) dev173666, dev173666. doi: 10.1242/dev.173666 |
