Dr Adam Ewing
Honorary Senior Fellow
Mater Research Institute-UQ, Faculty of Medicine
| Featured projects | Duration |
|---|---|
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Simultaneous identification of RNA-chromatin interactions and transcriptomes in single cells Genome Innovation Hub Collaborative Project (UQ infrastructure) |
2020 |
Book Chapter
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
Journal Articles
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
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
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
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
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
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
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
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
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
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
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. 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
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
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
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
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
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
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
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
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
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
Ewing, Adam D. (2015). Transposable element detection from whole genome sequence data. Mobile DNA, 6 (24) 24. doi: 10.1186/s13100-015-0055-3
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
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
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
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
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
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
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
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
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
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
Conference Paper
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.
Data Collection
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