Dr Ewing leads the Translational Bioinformatics Group at the Mater Research Institute - UQ, located at the Translational Research Institute (TRI). His research interests follow a common theme of developing and applying computational methods to investigate genomic mutation in evolutionary and disease-related processes. Dr Ewing is a key collaborator on an array of projects spanning from basic research into clinical applications of Bioinformatics.
Journal Article: Alpha cell receptor for advanced glycation end products associate with glucagon expression in type 1 diabetes
Leung, 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
Journal Article: Resolution of melanoma to PD-1 blockade but simultaneous rapid progression of concomitant chronic lymphocytic leukemia
Burgess, 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
Journal Article: Retrotransposon instability dominates the acquired mutation landscape of mouse induced pluripotent stem cells
Gerdes, 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
Long-read genetic and epigenetic profiling in lung cancer for precision medicine
(2021–2024) Priority-driven Collaborative Cancer Research Scheme
Mobile DNA activity in the mammalian primordial germline
(2021–2024) ARC Discovery Projects
The history of the human genome and the mechanisms of genomic disease
(2020–2024) NHMRC MRFF Investigator Grant
Applying long-read sequencing technologies to cancer genomes
Doctor Philosophy
Nanopore Sequencing for Mobile Element Research: The Long and Short of It
Doctor Philosophy
Epigenomic determinants of chemotherapy response in triple-negative breast cancer
Doctor Philosophy
The mobilisation of processed transcripts in germline and somatic tissues
Ewing, Adam D. (2017). The mobilisation of processed transcripts in germline and somatic tissues. Human retrotransposons in health and disease. (pp. 95-106) edited by Gael Cristofari. Cham, Switzerland: Springer. doi: 10.1007/978-3-319-48344-3_4
Leung, 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
Burgess, 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
Gerdes, 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
Sex-dependent differential transcript expression in the placenta of growth restricted infants
O'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
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
van 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
LINE-1 retrotransposon activation intrinsic to interneuron development
Bodea, 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.
Rasmussen, 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
No evidence of human genome integration of SARS-CoV-2 found by long-read DNA sequencing
Smits, 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
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
Multiscale imaging of basal cell dynamics in the functionally mature mammary gland
Stevenson, 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
Dawson, 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
Modulation of placental gene expression in small-for-gestational-age infants
O’Callaghan, Jessica L., Clifton, Vicki L., Prentis, Peter, Ewing, Adam, Miller, Yvette D. and Pelzer, Elise S. (2020). Modulation of placental gene expression in small-for-gestational-age infants. Genes, 11 (1) 80, 80. doi: 10.3390/genes11010080
A community effort to create standards for evaluating tumor subclonal reconstruction
Salcedo, Adriana, Tarabichi, Maxime, Espiritu, Shadrielle Melijah G., Deshwar, Amit G., David, Matei, Wilson, Nathan M., Dentro, Stefan, Wintersinger, Jeff A., Liu, Lydia Y., Ko, Minjeong, Sivanandan, Srinivasan, Zhang, Hongjiu, Zhu, Kaiyi, Ou Yang, Tai-Hsien, Chilton, John M., Buchanan, Alex, Lalansingh, Christopher M., P’ng, Christine, Anghel, Catalina V., Umar, Imaad, Lo, Bryan, Zou, William, Jha, Alokkumar, Huang, Tanxiao, Yang, Tsun-Po, Peifer, Martin, Sahinalp, Cenk, Malikic, Salem, Vázquez-García, Ignacio ... Boutros, Paul C. (2020). A community effort to create standards for evaluating tumor subclonal reconstruction. Nature Biotechnology, 38 (1), 97-107. doi: 10.1038/s41587-019-0364-z
He, Yaowu, Davies, Claire M., Harrington, Brittney S., Hellmers, Linh, Sheng, Yonghua, Broomfield, Amy, McGann, Thomas, Bastick, Kate, Zhong, Laurie, Wu, Andy, Maresh, Grace, McChesney, Shannon, Yau Wong, Kuan, Adams, Mark N., Sullivan, Ryan C., Palmer, James S., Burke, Lez J., Ewing, Adam D., Zhang, Xin, Margolin, David, Li, Li, Lourie, Rohan, Matsika, Admire, Srinivasan, Bhuvana, McGuckin, Michael A., Lumley, John W. and Hooper, John D. (2019). CDCP1 enhances Wnt signaling in colorectal cancer promoting nuclear localization of β-catenin and E-cadherin. Oncogene, 39 (1), 219-233. doi: 10.1038/s41388-019-0983-3
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
Dynamic methylation of an L1 transduction family during reprogramming and neurodifferentiation
Salvador-Palomeque, Carmen, Sanchez-Luque, Francisco J., Fortuna, Patrick R. J., Ewing, Adam D., Wolvetang, Ernst J., Richardson, Sandra R. and Faulkner, Geoffrey J. (2019). Dynamic methylation of an L1 transduction family during reprogramming and neurodifferentiation. Molecular and Cellular Biology, 39 (7) e00499-18, 1-19. doi: 10.1128/mcb.00499-18
Pugh, Carys A., Farrell, Lindsay L., Carlisle, Ailsa J., Bush, Stephen J., Ewing, Adam, Trejo-Reveles, Violeta, Matika, Oswald, de Kloet, Arne, Walsh, Caitlin, Bishop, Stephen C., Prendergast, James G. D., Rainger, Joe, Schoenebeck, Jeffrey J. and Summers, Kim M. (2019). Arginine to glutamine variant in olfactomedin like 3 (OLFML3) is a candidate for severe goniodysgenesis and glaucoma in the border collie dog breed. G3: Genes, Genomes, Genetics, 9 (3), 943-954. doi: 10.1534/g3.118.200944
Lee, Anna Y., Ewing, Adam D., Ellrott, Kyle, Hu, Yin, Houlahan, Kathleen E., Bare, J. Christopher, Espiritu, Shadrielle Melijah G., Huang, Vincent, Dang, Kristen, Chong, Zechen, Caloian, Cristian, Yamaguchi, Takafumi N., Kellen, Michael R., Chen, Ken, Norman, Thea C., Friend, Stephen H., Guinney, Justin, Stolovitzky, Gustavo, Haussler, David, Margolin, Adam A., Stuart, Joshua M. and Boutros, Paul C. (2018). Combining accurate tumor genome simulation with crowdsourcing to benchmark somatic structural variant detection. Genome Biology, 19 (1) 188, 188. doi: 10.1186/s13059-018-1539-5
Rare variants in Fanconi anemia genes are enriched in acute myeloid leukemia
Maung, Kyaw Ze Ya, Leo, Paul J., Bassal, Mahmoud, Casolari, Debora A., Gray, James X., Bray, Sarah C., Pederson, Stephen, Singhal, Deepak, Samaraweera, Saumya E., Nguyen, Tran, Cildir, Gökhan, Marshall, Mhairi, Ewing, Adam, Duncan, Emma L., Brown, Matthew A., Saal, Russell, Tergaonkar, Vinay, To, Luen Bik, Marlton, Paula, Gill, Devinder, Lewis, Ian, Deans, Andrew J., Brown, Anna L., D’Andrea, Richard J. and Gonda, Thomas J. (2018). Rare variants in Fanconi anemia genes are enriched in acute myeloid leukemia. Blood Cancer Journal, 8 (6) 50, 50. doi: 10.1038/s41408-018-0090-7
Human-specific NOTCH2NL genes affect notch signaling and cortical neurogenesis
Fiddes, Ian T., Lodewijk, Gerrald A., Mooring, Meghan, Bosworth, Colleen M., Ewing, Adam D., Mantalas, Gary L., Novak, Adam M., van den Bout, Anouk, Bishara, Alex, Rosenkrantz, Jimi L., Lorig-Roach, Ryan, Field, Andrew R., Haeussler, Maximilian, Russo, Lotte, Bhaduri, Aparna, Nowakowski, Tomasz J., Pollen, Alex A., Dougherty, Max L., Nuttle, Xander, Addor, Marie-Claude, Zwolinski, Simon, Katzman, Sol, Kriegstein, Arnold, Eichler, Evan E., Salama, Sofie R., Jacobs, Frank M.J. and Haussler, David (2018). Human-specific NOTCH2NL genes affect notch signaling and cortical neurogenesis. Cell, 173 (6), 1356-1369. doi: 10.1016/j.cell.2018.03.051
L1 retrotransposition is a common feature of mammalian hepatocarcinogenesis
Schauer, Stephanie N., Carreira, Patricia E., Shukla, Ruchi, Gerhardt, Daniel J., Gerdes, Patricia, Sanchez-Luque, Francisco J., Nicoli, Paola, Kindlova, Michaela, Ghisletti, Serena, Santos, Alexandre Dos, Rapoud, Delphine, Samuel, Didier, Faivre, Jamila, Ewing, Adam D., Richardson, Sandra R. and Faulkner, Geoffrey J. (2018). L1 retrotransposition is a common feature of mammalian hepatocarcinogenesis. Genome Research, 28 (5), 639-653. doi: 10.1101/gr.226993.117
Germline contamination and leakage in whole genome somatic single nucleotide variant detection
Sendorek, Dorota H., Caloian, Cristian, Ellrott, Kyle, Bare, J Christopher, Yamaguchi, Takafumi N., Ewing, Adam D., Houlahan, Kathleen E., Norman, Thea C., Margolin, Adam A., Stuart, Joshua M. and Boutros, Paul C. (2018). Germline contamination and leakage in whole genome somatic single nucleotide variant detection. BMC Bioinformatics, 19 (1) 28, 1-9. doi: 10.1186/s12859-018-2046-0
L1 retrotransposon heterogeneity in ovarian tumor cell evolution
Nguyen, Thu H. M., Carreira, Patricia E., Sanchez-Luque, Francisco J., Schauer, Stephanie N., Fagg, Allister C., Richardson, Sandra R., Davies, Claire M., Jesuadian, J. Samuel, Kempen, Marie-Jeanne H. C., Troskie, Robin-Lee, James, Cini, Beaven, Elizabeth A., Wallis, Tristan P., Coward, Jermaine I. G., Chetty, Naven P., Crandon, Alexander J., Venter, Deon J., Armes, Jane E., Perrin, Lewis C., Hooper, John D., Ewing, Adam D., Upton, Kyle R. and Faulkner, Geoffrey J. (2018). L1 retrotransposon heterogeneity in ovarian tumor cell evolution. Cell Reports, 23 (13), 3730-3740. doi: 10.1016/j.celrep.2018.05.090
On the role of H3.3 in retroviral silencing
Wolf, Gernot, Rebollo, Rita, Karimi, Mohammad M., Ewing, Adam D., Kamada, Rui, Wu, Warren, Wu, Brenda, Bachu, Mahesh, Ozato, Keiko, Faulkner, Geoffrey J., Mager, Dixie L., Lorincz, Matthew C. and Macfarlan, Todd S. (2017). On the role of H3.3 in retroviral silencing. Nature, 548 (7665), E1-E6. doi: 10.1038/nature23277
Analysis of LINE-1 elements in DNA from postmortem brains of individuals with schizophrenia
Doyle, Glenn A., Crist, Richard C., Karatas, Emre T., Hammond, Matthew J., Ewing, Adam D., Ferraro, Thomas N., Hahn, Chang-Gyu and Berrettini, Wade H. (2017). Analysis of LINE-1 elements in DNA from postmortem brains of individuals with schizophrenia. Neuropsychopharmacology, 42 (13), 2602-2611. doi: 10.1038/npp.2017.115
Heritable L1 retrotransposition in the mouse primordial germline and early embryo
Richardson, Sandra R., Gerdes, Patricia, Gerhardt, Daniel J., Sanchez-Luque, Francisco J., Bodea, Gabriela-Oana, Muñoz-Lopez, Martin, Jesuadian, J. Samuel, Kempen, Marie-Jeanne H. C., Carreira, Patricia E., Jeddeloh, Jeffrey A., Garcia-Perez, Jose L., Kazazian Jr., Haig H., Ewing, Adam D. and Faulkner, Geoffrey J. (2017). Heritable L1 retrotransposition in the mouse primordial germline and early embryo. Genome Research, 27 (8), 1395-1405. doi: 10.1101/gr.219022.116
Reading LINEs within the cocaine addicted brain
Doyle, Glenn A. , Doucet-O'Hare, Tara T. , Hammond, Matthew J. , Crist, Richard C. , Ewing, Adam D. , Ferraro, Thomas N. , Mash, Deborah C. , Kazazian, Haig H. and Berrettini, Wade H. (2017). Reading LINEs within the cocaine addicted brain. Brain and Behavior, 7 (5) e00678, e00678. doi: 10.1002/brb3.678
Carreira, Patricia E., Ewing, Adam D., Li, Guibo, Schauer, Stephanie N., Upton, Kyle R., Fagg, Allister C., Morell, Santiago, Kindlova, Michaela, Gerdes, Patricia, Richardson, Sandra R., Li, Bo, Gerhardt, Daniel J., Wang, Jun, Brennan, Paul M. and Faulkner, Geoffrey J. (2016). Evidence for L1-associated DNA rearrangements and negligible L1 retrotransposition in glioblastoma multiforme. Mobile DNA, 7 (1) 21, 1-14. doi: 10.1186/s13100-016-0076-6
Transposable element detection from whole genome sequence data
Ewing, Adam D. (2015). Transposable element detection from whole genome sequence data. Mobile DNA, 6 (24) 24. doi: 10.1186/s13100-015-0055-3
Widespread somatic L1 retrotransposition occurs early during gastrointestinal cancer evolution
Ewing, Adam D., Gacita, Anthony, Wood, Laura D., Ma, Florence, Xing, Dongmei, Kim, Min-Sik, Manda, Srikanth S., Abril, Gabriela, Pereira, Gavin, Makohon-Moore, Alvin, Looijenga, Leendert H.J., Gillis, Ad J.M., Hruban, Ralph H., Anders, Robert A., Romans, Katharine E., Pandey, Akhilesh, Iacobuzio-Donahue, Christine A., Vogelstein, Bert, Kinzler, Kenneth W., Kazazian, Haig H. and Solyom, Szilvia (2015). Widespread somatic L1 retrotransposition occurs early during gastrointestinal cancer evolution. Genome Research, 25 (10), 1536-1545. doi: 10.1101/gr.196238.115
Ewing, Adam D., Houlahan, Kathleen E., Hu, Yin, Ellrott, Kyle, Caloian, Cristian, Yamaguchi, Takafumi N., Bare, J. Christopher, P'Ng, Christine, Waggott, Daryl, Sabelnykova, Veronica Y., ICGC-TCGA DREAM Somatic Mutation Calling Challenge participants, Kellen, Michael R., Norman, Thea C., Haussler, David, Friend, Stephen H., Stolovitzky, Gustavo, Margolin, Adam A., Stuart, Joshua M. and Boutros, Paul C. (2015). Combining tumor genome simulation with crowdsourcing to benchmark somatic single-nucleotide-variant detection. Nature Methods, 12 (7), 623-630. doi: 10.1038/nmeth.3407
Ubiquitous L1 mosaicism in hippocampal neurons
Upton, Kyle R., Gerhardt, Daniel J., Jesuadian, J. Samuel, Richardson, Sandra R., Sanchez-Luque, Francisco J., Bodea, Gabriela O., Ewing, Adam D., Salvador-Palomeque, Carmen, van der Knaap, Mario S., Brennan, Paul M., Vanderver, Adeline and Faulkner, Geoffrey J. (2015). Ubiquitous L1 mosaicism in hippocampal neurons. Cell, 161 (2), 228-239. doi: 10.1016/j.cell.2015.03.026
An evolutionary arms race between KRAB zinc-finger genes ZNF91/93 and SVA/L1 retrotransposons
Jacobs, Frank M. J., Greenberg, David, Ngan Nguyen, Haeussler, Maximilian, Ewing, Adam D., Katzman, Sol, Paten, Benedict, Salama, Sofie R. and Haussler, David (2014). An evolutionary arms race between KRAB zinc-finger genes ZNF91/93 and SVA/L1 retrotransposons. Nature, 516 (7530), 242-245. doi: 10.1038/nature13760
RADIA: RNA and DNA integrated analysis for somatic mutation detection
Radenbaugh, Amie J., Ma, Singer, Ewing, Adam, Stuart, Joshua M., Collisson, Eric A., Zhu, Jingchun and Haussler, David (2014). RADIA: RNA and DNA integrated analysis for somatic mutation detection. PLoS ONE, 9 (11) e111516, e111516.1-e111516.11. doi: 10.1371/journal.pone.0111516
Boutros, Paul C., Ewing, Adam D., Ellrott, Kyle, Norman, Thea C., Dang, Kristen K., Hu, Yin, Kellen, Michael R., Suver, Christine, Bare, J. Christopher, Stein, Lincoln D., Spellman, Paul T., Stolovitzky, Gustavo, Friend, Stephen H., Margolin, Adam A. and Stuart, Joshua M. (2014). Global optimization of somatic variant identification in cancer genomes with a global community challenge. Nature Genetics, 46 (4), 318-319. doi: 10.1038/ng.2932
Retrotransposition of gene transcripts leads to structural variation in mammalian genomes
Ewing, Adam D., Ballinger, Tracy J., Earl, Dent, Harris, Christopher C., Ding, Li, Wilson, Richard K. and Haussler, David (2013). Retrotransposition of gene transcripts leads to structural variation in mammalian genomes. Genome Biology, 14 (3) R22. doi: 10.1186/gb-2013-14-3-r22
Enrichment of processed pseudogene transcripts in L1-ribonucleoprotein particles
Mandal, Prabhat K., Ewing, Adam D., Hancks, Dustin C. and Kazazian, Haig H., Jr. (2013). Enrichment of processed pseudogene transcripts in L1-ribonucleoprotein particles. Human Molecular Genetics, 22 (18) ddt225, 3730-3748. doi: 10.1093/hmg/ddt225
Extensive somatic L1 retrotransposition in colorectal tumors
Solyom, Szilvia, Ewing, Adam D., Rahrmann, Eric P., Doucet, Tara, Nelson, Heather H., Burns, Michael B., Harris, Reuben S., Sigmon, David F., Casella, Alex, Erlanger, Bracha, Wheelan, Sarah, Upton, Kyle R., Shukla, Ruchi, Faulkner, Geoffrey J., Largaespada, David A. and Kazazian, Haig H. (2012). Extensive somatic L1 retrotransposition in colorectal tumors. Genome Research, 22 (12), 2328-2338. doi: 10.1101/gr.145235.112
Pathogenic orphan transduction created by a nonreference LINE-1 retrotransposon
Solyom, Szilvia, Ewing, Adam D., Hancks, Dustin C., Takeshima, Yasuhiro, Awano, Hiroyuki, Matsuo, Masafumi and Kazazian, Haig H., Jr. (2012). Pathogenic orphan transduction created by a nonreference LINE-1 retrotransposon. Human Mutation, 33 (2), 369-371. doi: 10.1002/humu.21663
Whole-genome resequencing allows detection of many rare LINE-1 insertion alleles in humans
Ewing, Adam D. and Kazazian, Haig H., Jr. (2011). Whole-genome resequencing allows detection of many rare LINE-1 insertion alleles in humans. Genome Research, 21 (6), 985-990. doi: 10.1101/gr.114777.110
Ewing, Adam D. and Kazazian, Haig H., Jr. (2010). High-throughput sequencing reveals extensive variation in human-specific L1 content in individual human genomes. Genome Research, 20 (9), 1262-1270. doi: 10.1101/gr.106419.110
Exon-trapping mediated by the human retrotransposon SVA
Hancks, Dustin C., Ewing, Adam D., Chen, Jesse E., Tokunaga, Katsushi and Kazazian, Haig H. (2009). Exon-trapping mediated by the human retrotransposon SVA. Genome Research, 19 (11), 1983-1991. doi: 10.1101/gr.093153.109
Slater, Steven C., Goldman, Barry S., Goodner, Brad, Setubal, Joao C., Farrand, Stephen K., Nester, Eugene W., Burr, Thomas J., Banta, Lois, Dickerman, Allan W., Paulsen, Ian, Otten, Leon, Suen, Garret, Welch, Roy, Almeida, Nalvo F., Arnold, Frank, Burton, Oliver T., Du, Zijin, Ewing, Adam, Godsy, Eric, Heisel, Sara, Houmiel, Kathryn L., Jhaveri, Jinal, Lu, Jing, Miller, Nancy M., Norton, Stacie, Chen, Qiang, Phoolcharoen, Waranyoo, Ohlin, Victoria, Ondrusek, Dan ... Wood, Derek W. (2009). Genome sequences of three agrobacterium biovars help elucidate the evolution of multichromosome genomes in bacteria. Journal of Bacteriology, 191 (8), 2501-2511. doi: 10.1128/JB.01779-08
Bai, Xiaodong, Zhang, Jianhua, Ewing, Adam, Miller, Sally A., Radek, Agnes Jancso, Shevchenko, Dmitriy V., Tsukerman, Kiryl, Walunas, Theresa, Lapidus, Alla, Campbell, John W. and Hogenhout, Saskia A. (2006). Living with genome instability: The adaptation of phytoplasmas to diverse environments of their insect and plant hosts. Journal of Bacteriology, 188 (10), 3682-3696. doi: 10.1128/JB.188.10.3682-3696.2006
O'Callaghan, Jessica, Clifton, Vicki, Prentis, Peter, Ewing, Adam and Pelzer, Elise (2021). Maternal clinical characteristics have unique effects on placental function that are distinct based on fetal growth. London, United Kingdom: Elsevier. doi: 10.1016/j.placenta.2021.07.194
Csonka, LN, O'Connor, K, Larimer, F, Richardson, P, Lapidus, A, Ewing, AD, Goodner, BW and Oren, A (2005). What we can deduce about metabolism in the moderate halophile Chromohalobacter salexigens from its genomic sequence. Halophiles 2004 International Symposium, Ljubljana Slovenia, Sep 04-09, 2004. SPRINGER.
Lockett, Jack , Saif, Zarqa, Nolan, Brendan J., Keshvari, Sahar, Cesana-Nigro, Nicole, Ewing, Adam, Inder, Warrick J. and Clifton, Vicki L. (2022). Glucocorticoid activity regulates glucocorticoid receptor isoform expression and downstream gene transcription in humans. The University of Queensland. (Dataset) doi: 10.48610/ee0c38e
Long-read genetic and epigenetic profiling in lung cancer for precision medicine
(2021–2024) Priority-driven Collaborative Cancer Research Scheme
Mobile DNA activity in the mammalian primordial germline
(2021–2024) ARC Discovery Projects
The history of the human genome and the mechanisms of genomic disease
(2020–2024) NHMRC MRFF Investigator Grant
Unlocking the cellular determinants of retrotransposition
(2017–2018) ARC Discovery Projects
The functional impact of new genes acquired through retrotransposition
(2015–2018) ARC Discovery Early Career Researcher Award
Functional annotation of structural variants in human genetic disease
(2015) UQ Early Career Researcher
Applying long-read sequencing technologies to cancer genomes
Doctor Philosophy — Principal Advisor
Other advisors:
Nanopore Sequencing for Mobile Element Research: The Long and Short of It
Doctor Philosophy — Associate Advisor
Other advisors:
Epigenomic determinants of chemotherapy response in triple-negative breast cancer
Doctor Philosophy — Associate Advisor
Other advisors:
Development of predictive models for adverse perinatal and maternal outcomes in late gestation pregnancies applying machine learning algorithms.
Doctor Philosophy — Associate Advisor
Other advisors:
Mobile DNA Activity in the Mammalian Primordial Germline
Doctor Philosophy — Associate Advisor
Other advisors:
Longitudinal evaluation of glucocorticoid receptor isoforms and glucocorticoid responsive genes in medical patients on prednisolone.
Doctor Philosophy — Associate Advisor
Other advisors:
(2023) Doctor Philosophy — Associate Advisor
Other advisors:
Functional coding and noncoding pseudogenes in the human genome
(2022) Doctor Philosophy — Associate Advisor
Other advisors:
Note for students: The possible research projects listed on this page may not be comprehensive or up to date. Always feel free to contact the staff for more information, and also with your own research ideas.
Developing software to support Cancer Genomics