The University of Queensland

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

Modulation of placental gene expression in small-for-gestational-age infants

O’Callaghan, Jessica L., Vicki Clifton, 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.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, Mustonen, Ville, Yang, Hsih-Te, Lee, Ken-Ray, Ji, Yuan, Sengupta, Subhajit, Rudewicz, Justine, Nikolski, Macha, Schaeverbeke, Quentin, Yuan, Ke, Markowetz, Florian, Macintyre, Geoff, Cmero, Marek, Chaudhary, Belal, Leshchiner, Ignaty, Livitz, Dimitri, Getz, Gad, Loher, Phillipe, Yu, Kaixian, Wang, Wenyi, Zhu, Hongtu, Simpson, Jared T., Stuart, Joshua M., Anastassiou, Dimitris, Guan, Yuanfang, Ewing, Adam D., Ellrott, Kyle, Wedge, David C., Morris, Quaid, Van Loo, Peter and 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

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, 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: . doi:10.1128/mcb.00499-18

Arginine to glutamine variant in olfactomedin like 3 (OLFML3) is a candidate for severe goniodysgenesis and glaucoma in the border collie dog breed

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

Combining accurate tumor genome simulation with crowdsourcing to benchmark somatic structural variant detection

Lee, Anna Y., Ewing, Adam, 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

Evidence for L1-associated DNA rearrangements and negligible L1 retrotransposition in glioblastoma multiforme

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

Combining tumor genome simulation with crowdsourcing to benchmark somatic single-nucleotide-variant detection

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

Global optimization of somatic variant identification in cancer genomes with a global community challenge

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

High-throughput sequencing reveals extensive variation in human-specific L1 content in individual human genomes

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

Genome sequences of three agrobacterium biovars help elucidate the evolution of multichromosome genomes in bacteria

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

Living with genome instability: The adaptation of phytoplasmas to diverse environments of their insect and plant hosts

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

What we can deduce about metabolism in the moderate halophile Chromohalobacter salexigens from its genomic sequence

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.