The University of Queensland

Long-read cDNA sequencing identifies functional pseudogenes in the human transcriptome

Troskie, 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

Nanopore sequencing enables comprehensive transposable element epigenomic profiling

Ewing, 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

Overcoming challenges and dogmas to understand the functions of pseudogenes

Cheetham, 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

RNA-DamID reveals cell-type-specific binding of roX RNAs at chromatin-entry sites

Cheetham, 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

Mapping RNA-Chromatin interactions in vivo with RNA-DamID

Cheetham, 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

HOPX-associated molecular programs control cardiomyocyte cell states underpinning cardiac structure and function

Friedman, 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

Vasculature organotropism in drug delivery

Amruta, 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

mRNA vaccine quality analysis using RNA sequencing

Gunter, 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

Somatic retrotransposition in the developing rhesus macaque brain

Billon, 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

Methylartist: tools for visualizing modified bases from nanopore sequence data

Cheetham, 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

Reduced chromatin accessibility correlates with resistance to Notch activation

van 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

In vivo targeted DamID identifies CHD8 genomic targets in fetal mouse brain

Wade, 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

Processed pseudogenes: a substrate for evolutionary innovation. Retrotransposition contributes to genome evolution by propagating pseudogene sequences with rich regulatory potential throughout the genome

Troskie, 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

Long-read cDNA sequencing identifies functional pseudogenes in the human transcriptome

Troskie, 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

Microdeletion of 9q22.3: a patient with minimal deletion size associated with a severe phenotype

Ewing, 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

Nanopore sequencing enables comprehensive transposable element epigenomic profiling

Ewing, 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

Overcoming challenges and dogmas to understand the functions of pseudogenes

Cheetham, 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

LINE-1 Evasion of epigenetic repression in humans

Sanchez-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

DamID as a versatile tool for understanding gene regulation

Aughey, 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

Targeted DamID reveals differential binding of mammalian pluripotency factors

Cheetham, Seth W., Gruhn, Wolfram H., van den Ameele, Jelle, Krautz, Robert, Southall, Tony D., Kobayashi, Toshihiro, Surani, M. Azim and Brand, Andrea H. (2018). Targeted DamID reveals differential binding of mammalian pluripotency factors. Development, 145 (20) dev170209, dev.170209. doi: 10.1242/dev.170209

RNA-DamID reveals cell-type-specific binding of roX RNAs at chromatin-entry sites

Cheetham, 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

High resolution temporal transcriptomics of mouse embryoid body development reveals complex expression dynamics of coding and noncoding loci

Gloss, Brian S., Signal, Bethany, Cheetham, Seth W., Gruhl, Franziska, Kaczorowski, Dominik C., Perkins, Andrew C. and Dinger, Marcel E. (2017). High resolution temporal transcriptomics of mouse embryoid body development reveals complex expression dynamics of coding and noncoding loci. Scientific Reports, 7 (1) 6731, 6731. doi: 10.1038/s41598-017-06110-5

Cell-type-specific profiling of protein-DNA interactions without cell isolation using targeted DamID with next-generation sequencing

Marshall, Owen J., Southall, Tony D., Cheetham, Seth W. and Brand, Andrea H. (2016). Cell-type-specific profiling of protein-DNA interactions without cell isolation using targeted DamID with next-generation sequencing. Nature Protocols, 11 (9), 1586-1598. doi: 10.1038/nprot.2016.084

The Evx1/Evx1as gene locus regulates anterior-posterior patterning during gastrulation

Bell, Charles C., Amaral, Paulo P., Kalsbeek, Anton, Magor, Graham W., Gillinder, Kevin R., Tangermann, Pierre, di Lisio, Lorena, Cheetham, Seth W., Gruhl, Franziska, Frith, Jessica, Tallack, Michael R., Ru, Ke-Lin, Crawford, Joanna, Mattick, John S., Dinger, Marcel E. and Perkins, Andrew C. (2016). The Evx1/Evx1as gene locus regulates anterior-posterior patterning during gastrulation. Scientific Reports, 6 (1) 26657, 26657. doi: 10.1038/srep26657

Freedom of expression: cell-type-specific gene profiling

Otsuki, Leo, Cheetham, Seth W. and Brand, Andrea H. (2014). Freedom of expression: cell-type-specific gene profiling. Wiley Interdisciplinary Reviews: Developmental Biology, 3 (6), 429-443. doi: 10.1002/wdev.149

Long noncoding RNAs and the genetics of cancer

Cheetham, S. W., Gruhl, F., Mattick, J. S. and Dinger, M. E. (2013). Long noncoding RNAs and the genetics of cancer. British Journal of Cancer, 108 (12), 2419-2425. doi: 10.1038/bjc.2013.233

Insulin finds its niche

Cheetham, Seth W. and Brand, Andrea H. (2013). Insulin finds its niche. Science, 340 (6134), 817-818. doi: 10.1126/science.1238525

Pinstripe: a suite of programs for integrating transcriptomic and proteomic datasets identifies novel proteins and improves differentiation of protein-coding and non-coding genes

Gascoigne, Dennis K., Cheetham, Seth W., Cattenoz, Pierre B., Clark, Michael B., Amaral, Paulo P., Taft, Ryan J., Wilhelm, Dagmar, Dinger, Marcel E. and Mattick, John S. (2012). Pinstripe: a suite of programs for integrating transcriptomic and proteomic datasets identifies novel proteins and improves differentiation of protein-coding and non-coding genes. Bioinformatics, 28 (23), 3042-3050. doi: 10.1093/bioinformatics/bts582