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2024 Journal Article Molecular genetic analysis of candidate genes for glutaric aciduria type II in a cohort of patients from Queensland, AustraliaDemetriou, Kalliope, Nisbet, Janelle, Coman, David, Ewing, Adam D., Phillips, Liza, Smith, Sally, Lipke, Michelle, Inwood, Anita, Spicer, Janette, Atthow, Catherine, Wilgen, Urs, Robertson, Thomas, McWhinney, Avis, Swenson, Rebecca, Espley, Brayden, Snowdon, Brianna, McGill, James J. and Summers, Kim M. (2024). Molecular genetic analysis of candidate genes for glutaric aciduria type II in a cohort of patients from Queensland, Australia. Molecular Genetics and Metabolism, 142 (4) 108516, 1-14. doi: 10.1016/j.ymgme.2024.108516 |
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2024 Journal Article LINE-1 retrotransposons contribute to mouse PV interneuron developmentBodea, Gabriela O., Botto, Juan M., Ferreiro, Maria E., Sanchez-Luque, Francisco J., de los Rios Barreda, Jose, Rasmussen, Jay, Rahman, Muhammed A., Fenlon, Laura R., Jansz, Natasha, Gubert, Carolina, Gerdes, Patricia, Bodea, Liviu-Gabriel, Ajjikuttira, Prabha, Da Costa Guevara, Darwin J., Cumner, Linda, Bell, Charles C., Kozulin, Peter, Billon, Victor, Morell, Santiago, Kempen, Marie-Jeanne H. C., Love, Chloe J., Saha, Karabi, Palmer, Lucy M., Ewing, Adam D., Jhaveri, Dhanisha J., Richardson, Sandra R., Hannan, Anthony J. and Faulkner, Geoffrey J. (2024). LINE-1 retrotransposons contribute to mouse PV interneuron development. Nature Neuroscience, 27 (7), 1-34. doi: 10.1038/s41593-024-01650-2 |
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2024 Journal Article Placentae of small appropriately-grown-for-gestational-age neonates exhibit sexually dimorphic transcriptomic changes representative of placental insufficiencyEwing, Adam, O'Callaghan, Jessica L., McCracken, Sharon, Ellery, Stacy, Lappas, Martha, Holland, Olivia J., Perkins, Anthony, Saif, Zarqa and Clifton, Vicki L. (2024). Placentae of small appropriately-grown-for-gestational-age neonates exhibit sexually dimorphic transcriptomic changes representative of placental insufficiency. Placenta, 149, 37-43. doi: 10.1016/j.placenta.2024.02.003 |
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2023 Journal Article Vitamin C activates young LINE-1 elements in mouse embryonic stem cells via H3K9me3 demethylationCheng, Kevin C. L., Frost, Jennifer M., Sánchez-Luque, Francisco J., García-Canãdas, Marta, Taylor, Darren, Yang, Wan R., Irayanar, Branavy, Sampath, Swetha, Patani, Hemalvi, Agger, Karl, Helin, Kristian, Ficz, Gabriella, Burns, Kathleen H., Ewing, Adam, García-Pérez, José L. and Branco, Miguel R. (2023). Vitamin C activates young LINE-1 elements in mouse embryonic stem cells via H3K9me3 demethylation. Epigenetics and Chromatin, 16 (1) 39, 1-16. doi: 10.1186/s13072-023-00514-6 |
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2023 Journal Article Locus-resolution analysis of L1 regulation and retrotransposition potential in mouse embryonic developmentGerdes, Patricia, Chan, Dorothy, Lundberg, Mischa, Sanchez-Luque, Francisco J., Bodea, Gabriela O., Ewing, Adam D., Faulkner, Geoffrey J. and Richardson, Sandra R. (2023). Locus-resolution analysis of L1 regulation and retrotransposition potential in mouse embryonic development. Genome Research, 33 (9), 1465-1481. doi: 10.1101/gr.278003.123 |
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2023 Journal Article Alpha cell receptor for advanced glycation end products associate with glucagon expression in type 1 diabetesLeung, Sherman S., Lenchik, Nataliya, Mathews, Clayton, Pugliese, Alberto, McCarthy, Domenica A., Le Bagge, Selena, Ewing, Adam, Harris, Mark, Radford, Kristen J., Borg, Danielle J., Gerling, Ivan and Forbes, Josephine M. (2023). Alpha cell receptor for advanced glycation end products associate with glucagon expression in type 1 diabetes. Scientific Reports, 13 (1) 12948, 1-15. doi: 10.1038/s41598-023-39243-x |
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2023 Journal Article Resolution of melanoma to PD-1 blockade but simultaneous rapid progression of concomitant chronic lymphocytic leukemiaBurgess, Melinda, Keane, Colm, Tobin, Joshua W. D., Law, Soi Cheng, Griffin, Alison, Gill, Devinder, Ewing, Adam D., Atkinson, Victoria, Mollee, Peter, Sabdia, Muhammed B., Saunders, Nicholas and Gandhi, Maher K. (2023). Resolution of melanoma to PD-1 blockade but simultaneous rapid progression of concomitant chronic lymphocytic leukemia. Acta Haematologica, 146 (2), 166-171. doi: 10.1159/000527631 |
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2022 Journal Article Retrotransposon instability dominates the acquired mutation landscape of mouse induced pluripotent stem cellsGerdes, Patricia, Lim, Sue Mei, Ewing, Adam D., Larcombe, Michael R., Chan, Dorothy, Sanchez-Luque, Francisco J., Walker, Lucinda, Carleton, Alexander L., James, Cini, Knaupp, Anja S., Carreira, Patricia E., Nefzger, Christian M., Lister, Ryan, Richardson, Sandra R., Polo, Jose M. and Faulkner, Geoffrey J. (2022). Retrotransposon instability dominates the acquired mutation landscape of mouse induced pluripotent stem cells. Nature Communications, 13 (1) 7470, 1-18. doi: 10.1038/s41467-022-35180-x |
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2022 Journal Article Sex-dependent differential transcript expression in the placenta of growth restricted infantsO'Callaghan, Jessica L., Clifton, Vicki L., Prentis, Peter, Ewing, Adam, Saif, Zarqa and Pelzer, Elise S. (2022). Sex-dependent differential transcript expression in the placenta of growth restricted infants. Placenta, 128, 1-8. doi: 10.1016/j.placenta.2022.08.004 |
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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 A hidden layer of structural variation in transposable elements reveals potential genetic modifiers in human disease-risk locivan Bree, Elisabeth J, Guimarães, Rita L F P, Lundberg, Mischa, Blujdea, Elena R, Rosenkrantz, Jimi L, White, Fred T G, Poppinga, Josse, Ferrer-Raventós, Paula, Schneider, Anne-Fleur E, Clayton, Isabella, Haussler, David, Reinders, Marcel J T, Holstege, Henne, Ewing, Adam D, Moses, Colette and Jacobs, Frank M J (2022). A hidden layer of structural variation in transposable elements reveals potential genetic modifiers in human disease-risk loci. Genome research, 32 (4), 656-670. doi: 10.1101/gr.275515.121 |
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2022 Journal Article LINE-1 retrotransposon activation intrinsic to interneuron developmentBodea, Gabriela O., Ferreiro, Maria E., Sanchez-Luque, Francisco J., Botto, Juan M., Rasmussen, Jay, Rahman, Muhammed A., Fenlon, Laura R., Gubert, Carolina, Gerdes, Patricia, Bodea, Liviu-Gabriel, Ajjikuttira, Prabha, Kozulin, Peter, Billon, Victor, Morell, Santiago, Kempen, Marie-Jeanne H.C., Love, Chloe J., Palmer, Lucy M., Ewing, Adam D., Jhaveri, Dhanisha J., Richardson, Sandra R., Hannan, Anthony J. and Faulkner, Geoffrey J. (2022). LINE-1 retrotransposon activation intrinsic to interneuron development. |
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2021 Journal Article An early proinflammatory transcriptional response to tau pathology is age‐specific and foreshadows reduced tau burdenRasmussen, Jay, Ewing, Adam D., Bodea, Liviu‐Gabriel, Bodea, Gabriela O., Gearing, Marla and Faulkner, Geoffrey J. (2021). An early proinflammatory transcriptional response to tau pathology is age‐specific and foreshadows reduced tau burden. Brain Pathology, 32 (3) e13018, e13018. doi: 10.1111/bpa.13018 |
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2021 Journal Article No evidence of human genome integration of SARS-CoV-2 found by long-read DNA sequencingSmits, Nathan, Rasmussen, Jay, Bodea, Gabriela O., Amarilla, Alberto A., Gerdes, Patricia, Sanchez-Luque, Francisco J., Ajjikuttira, Prabha, Modhiran, Naphak, Liang, Benjamin, Faivre, Jamila, Deveson, Ira W., Khromykh, Alexander A., Watterson, Daniel, Ewing, Adam D. and Faulkner, Geoffrey J. (2021). No evidence of human genome integration of SARS-CoV-2 found by long-read DNA sequencing. Cell Reports, 36 (7) 109530, 109530. doi: 10.1016/j.celrep.2021.109530 |
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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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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 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 Multiscale imaging of basal cell dynamics in the functionally mature mammary glandStevenson, Alexander J., Vanwalleghem, Gilles, Stewart, Teneale A., Condon, Nicholas D., Lloyd-Lewis, Bethan, Marino, Natascia, Putney, James W., Scott, Ethan K., Ewing, Adam D. and Davis, Felicity M. (2020). Multiscale imaging of basal cell dynamics in the functionally mature mammary gland. Proceedings of the National Academy of Sciences, 117 (43), 1-11. doi: 10.1073/pnas.2016905117 |
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2020 Journal Article Whole genome investigation of an atypical autism case identifies a novel ANOS1 mutation with subsequent diagnosis of Kallmann syndromeDawson, Paul A., Lee, Soohyun, Ewing, Adam D., Prins, Johannes B. and Heussler, Helen S. (2020). Whole genome investigation of an atypical autism case identifies a novel ANOS1 mutation with subsequent diagnosis of Kallmann syndrome. Molecular Genetics and Metabolism Reports, 23 100593, 100593. doi: 10.1016/j.ymgmr.2020.100593 |
