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.
Journal Article: CDCP1 enhances Wnt signaling in colorectal cancer promoting nuclear localization of β-catenin and E-cadherin
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, . doi:10.1038/s41388-019-0983-3
Journal Article: 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
Journal Article: 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: . doi:10.1128/mcb.00499-18
The history of the human genome and the mechanisms of genomic disease
(2020–2024) NHMRC Investigator Grants
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
Machine learning models for non-coding mutation impact prediction
Doctor Philosophy
Deciphering global and locus-specific regulation of LINE-1 (L1) retrotransposons in cancer
Doctor Philosophy
The role of pseudogenes in human biology and cancer
Doctor Philosophy
Understanding how cells regulate mobile DNA
Mutation impact prediction in in the non-coding genome
Developing software to support Cancer Genomics
The mobilisation of processed transcripts in germline and somatic tissues
Ewing, Adam D. (2017). The mobilisation of processed transcripts in germline and somatic tissues. In Gael Cristofari (Ed.), Human retrotransposons in health and disease (pp. 95-106) Cham, Switzerland: Springer. doi:10.1007/978-3-319-48344-3_4
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, . 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: . 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. 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. 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: 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. 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
Transposable element detection from whole genome sequence data
Ewing, Adam D. (2015) Transposable element detection from whole genome sequence data. Mobile DNA, 6 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: e111516.1-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: . 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: 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, 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
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. In: Adaptation to Life at High Salt Concentrations in Archaea, Bacteria, and Eukarya. Halophiles 2004 International Symposium, Ljubljana Slovenia, (267-+). Sep 04-09, 2004.
The history of the human genome and the mechanisms of genomic disease
(2020–2024) NHMRC Investigator Grants
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
Machine learning models for non-coding mutation impact prediction
Doctor Philosophy — Associate Advisor
Other advisors:
Deciphering global and locus-specific regulation of LINE-1 (L1) retrotransposons in cancer
Doctor Philosophy — Associate Advisor
Other advisors:
The role of pseudogenes in human biology and cancer
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.
Understanding how cells regulate mobile DNA
Mutation impact prediction in in the non-coding genome
Developing software to support Cancer Genomics