Dr Adam Ewing

ARC DECRA

Mater Research Institute-UQ
Faculty of Medicine

Overview

I lead the Translational Bioinformatics Group at the Mater Research Institute - UQ, located at the TRI. My research interests follow a common theme of applying computational methods to investigate the biological mechanisms of mutation in evolutionary and disease-related processes.

I started out academically obtaining a Bachelor's degree in both Biology and Computer Science from Hiram College in Hiram, Ohio (USA), followed by earning a PhD in Genomics and Computational Biology at the University of Pennsylvania School of Medicine (2010). After completing postdoctoral experience at The Johns Hopkins University School of Medicine and The University of California Santa Cruz, I moved to Brisbane in early 2014 to join the Mater Research Institute. I was successful in obtaining a Discovery Early Career Research Award fellowship from the Australian Research Council beginning in 2015 and a Discovery Project Grant from the ARC beginning 2017.

Research Interests

  • Detecting and interpreting mutations
  • The genomic biology of retrotransposition

Qualifications

  • Doctor of Philosophy, University of Pennsylvania

Publications

  • 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

  • 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, Haig H. Jr, 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: . doi:10.1002/brb3.678

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Grants

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Available Projects

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Publications

Book Chapter

Journal Article

  • 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

  • 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, Haig H. Jr, 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: . 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: 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: . 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: e111516.1-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: . 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: 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, Pride, Nicole, Stricklin, Shawn L., Sun, Jian, Wheeler, Cathy, Wilson, Lindsey, Zhu, Huijun and 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 Publication

Grants (Administered at UQ)

Possible Research Projects

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.