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2016 Journal Article TET enzymes: double agents in the transposable element-host genome conflictGerdes, Patricia, Richardson, Sandra R. and Faulkner, Geoffrey J. (2016). TET enzymes: double agents in the transposable element-host genome conflict. Genome Biology, 17 (1) 259. doi: 10.1186/s13059-016-1124-8 |
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2016 Journal Article Evidence for L1-associated DNA rearrangements and negligible L1 retrotransposition in glioblastoma multiformeCarreira, 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 |
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2016 Journal Article Transposable elements in the mammalian embryo: pioneers surviving through stealth and serviceGerdes, Patricia, Richardson, Sandra R., Mager, Dixie L. and Faulkner, Geoffrey J. (2016). Transposable elements in the mammalian embryo: pioneers surviving through stealth and service. Genome Biology, 17 (1) 100. doi: 10.1186/s13059-016-0965-5 |
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2016 Journal Article Point mutations in Exon 1B of APC Reveal Gastric Adenocarcinoma and Proximal Polyposis of the Stomach as a Familial Adenomatous Polyposis VariantLi, Jun, Woods, Susan L., Healey, Sue, Beesley, Jonathan, Chen, Xiaoqing, Lee, Jason S., Sivakumaran, Haran, Wayte, Nicci, Nones, Katia, Waterfall, Joshua J., Pearson, John, Patch, Anne-Marie, Senz, Janine, Ferreira, Manuel A., Kaurah, Pardeep, Mackenzie, Robertson, Heravi-Moussavi, Alireza, Hansford, Samantha, Lannagan, Tamsin R. M., Spurdle, Amanda B., Simpson, Peter T., da Silva, Leonard, Lakhani, Sunil R., Clouston, Andrew D., Bettington, Mark, Grimpen, Florian, Busuttil, Rita A., Di Costanzo, Natasha, Boussioutas, Alex ... Chenevix-Trench, Georgia (2016). Point mutations in Exon 1B of APC Reveal Gastric Adenocarcinoma and Proximal Polyposis of the Stomach as a Familial Adenomatous Polyposis Variant. American Journal of Human Genetics, 98 (5), 830-842. doi: 10.1016/j.ajhg.2016.03.001 |
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2016 Journal Article Reprogramming triggers endogenous L1 and Alu retrotransposition in human induced pluripotent stem cellsKlawitter, Sabine, Fuchs,Nina V., Upton, Kyle R., Munoz-Lopez, Martin, Shukla, Ruchi, Wang, Jichang, Garcia-Canadas, Marta, Lopez-Ruiz, Cesar, Gerhardt, Daniel J., Sebe, Attila, Grabundzija, Ivana, Merkert, Sylvia, Gerdes, Patricia, Pulgarin, J. Andres, Bock, Anja, Held, Ulrike, Witthuhn, Anett, Haase, Alexandra, Sarkadi, Balazs, Lower, Johannes, Wolvetang, Ernst J., Martin, Ulrich, Ivics, Zoltan, Izsvak, Zsuzsanna, Garcia-Perez, Jose L., Faulkner, Geoffrey J. and Schumann, Gerald G. (2016). Reprogramming triggers endogenous L1 and Alu retrotransposition in human induced pluripotent stem cells. Nature Communications, 7 (1) 10286, 1-14. doi: 10.1038/ncomms10286 |
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2016 Book Chapter Retrotransposon capture sequencing (RC-Seq): a targeted, high-throughput approach to resolve somatic L1 retrotransposition in humansSanchez-Luque, Francisco J., Richardson, Sandra R. and Faulkner, Geoffrey J. (2016). Retrotransposon capture sequencing (RC-Seq): a targeted, high-throughput approach to resolve somatic L1 retrotransposition in humans. Transposons and retrotranspons: methods and protocols. (pp. 47-77) edited by Jose L. Garcia-Pérez. New York, NY, United States: Springer. doi: 10.1007/978-1-4939-3372-3_4 |
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2015 Journal Article Ubiquitous L1 mosaicism in hippocampal neuronsUpton, 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 |
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2015 Journal Article Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cellsArner, Erik, Daub, Carsten O., Vitting-Seerup, Kristoffer, Andersson, Robin, Lilje, Berit, Drabløs, Finn, Lennartsson, Andreas, Rönnerblad, Michelle, Hrydziuszko, Olga, Vitezic, Morana, Freeman, Tom C., Alhendi, Ahmad M. N., Arner, Peter, Axton, Richard, Baillie, J. Kenneth, Beckhouse, Anthony, Bodega, Beatrice, Briggs, James, Brombacher, Frank, Davis, Margaret, Detmar, Michael, Ehrlund, Anna, Endoh, Mitsuhiro, Eslami, Afsaneh, Fagiolini, Michela, Fairbairn, Lynsey, Faulkner, Geoffrey J., Ferrai, Carmelo, Fisher, Malcolm E. ... Hayashizaki, Yoshihide (2015). Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells. Science, 347 (6225), 1010-1014. doi: 10.1126/science.1259418 |
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2014 Journal Article L1 retrotransposons and somatic mosaicism in the brainRichardson, Sandra R., Morell, Santiago and Faulkner, Geoffrey J. (2014). L1 retrotransposons and somatic mosaicism in the brain. Annual Review of Genetics, 48, 1-27. doi: 10.1146/annurev-genet-120213-092412 |
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2014 Journal Article Blood from 'junk': the LTR chimeric transcript Pu.2 promotes erythropoiesisUpton, Kyle R. and Faulkner,Geoffrey J. (2014). Blood from 'junk': the LTR chimeric transcript Pu.2 promotes erythropoiesis. Mobile DNA, 5 (1) 15, 15. doi: 10.1186/1759-8753-5-15 |
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2014 Journal Article NanoCAGE analysis of the mouse olfactory epithelium identifies the expression of vomeronasal receptors and of proximal LINE elementsPascarella, Giovanni, Lazarevic, Dejan, Plessy, Charles, Bertin, Nicolas, Akalin, Altuna, Vlachouli, Christina, Simone, Roberto, Faulkner, Geoffry J., Zucchelli, Silvia, Kawai, Jun, Daub, Carsten O., Hayashizaki, Yoshihide, Lenhard, Boris, Carninci, Piero and Gustincich, Stefano (2014). NanoCAGE analysis of the mouse olfactory epithelium identifies the expression of vomeronasal receptors and of proximal LINE elements. Frontiers in Cellular Neuroscience, 8 (FEB) 41, 41. doi: 10.3389/fncel.2014.00041 |
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2014 Journal Article Diversity through duplication: Whole-genome sequencing reveals novel gene retrocopies in the human populationRichardson, Sandra R., Salvador-Palomeque, Carmen and Faulkner, Geoffrey J. (2014). Diversity through duplication: Whole-genome sequencing reveals novel gene retrocopies in the human population. BioEssays, 36 (5), 475-481. doi: 10.1002/bies.201300181 |
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2014 Journal Article L1 retrotransposons, cancer stem cells and oncogenesisCarreira, Patricia E., Richardson, Sandra R. and Faulkner, Geoffrey J. (2014). L1 retrotransposons, cancer stem cells and oncogenesis. FEBS Journal, 281 (1), 63-73. doi: 10.1111/febs.12601 |
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2014 Journal Article A promoter-level mammalian expression atlasForest, Alistair R. R., Kawaji, Hideya, Rehli, Michael, Baillie, J. Kenneth, De Hoon, Michael J. L., Haberle, Vanja, Lassmann, Timo, Kulakovskiy, Ivan V., Lizio, Marina, Itoh, Masayoshi, Andersson, Robin, Mungall, Christopher J., Meehan, Terrence F., Schmeier, Sebastian, Bertin, Nicholas, Jorgensen, Mette, Dimont, Emmanuel, Arner, Erik, Schmidl, Christian, Schaefer, Ulf, Medvedeva, Yulia A., Plessy, Charles, Vitezic, Morana, Severin, Jessica, Semple, Colin A., Ishizu, Yuri, Young, Robert S., Francescatto, Margherita, Altschuler, Intikhab ... Hayashizaki, Yoshihide (2014). A promoter-level mammalian expression atlas. Nature, 507 (7493), 462-470. doi: 10.1038/nature13182 |
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2014 Conference Publication Line-1, a novel biomarker for high-grade serous ovarian carcinomaNguyen, T. H. M., Upton, K. R. and Faulkner, G. J. (2014). Line-1, a novel biomarker for high-grade serous ovarian carcinoma. 15th Biennial Meeting of the International Gynecologic Cancer Society, Melbourne, Australia, 8 -11 November 2014. New York, United States: Lippincott Williams & Wilkins. doi: 10.1097/01.IGC.0000457075.08973.89 |
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2013 Journal Article Retrotransposon Silencing During Embryogenesis: Dicer Cuts in LINEFaulkner, Geoffrey J. (2013). Retrotransposon Silencing During Embryogenesis: Dicer Cuts in LINE. PLoS Genetics, 9 (11) e1003944, e1003944. doi: 10.1371/journal.pgen.1003944 |
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2013 Journal Article Genome-wide methylated CpG island profiles of melanoma cells reveal a melanoma coregulation networkLi, Jian-Liang, Mazar, Joseph, Zhong, Cuncong, Faulkner, Geoffrey J., Govindarajan, Subramaniam S., Zhang, Zhan, Dinger, Marcel E., Meredith, Gavin, Adams, Christopher, Zhang, Shaojie, Mattick, John S., Ray, Animesh and Perera, Ranjan J. (2013). Genome-wide methylated CpG island profiles of melanoma cells reveal a melanoma coregulation network. Scientific Reports, 3 (1) 2962, 02962.1-02962.12. doi: 10.1038/srep02962 |
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2013 Journal Article Endogenous retrotransposition activates oncogenic pathways in hepatocellular carcinomaShukla, Ruchi, Upton, Kyle R., Muñoz-Lopez, Martin, Gerhardt, Daniel J., Fisher, Malcolm E., Thu Nguyen, Brennan, Paul M., Baillie, J. Kenneth, Collino, Agnese, Ghisletti, Serena, Sinha, Shruti, Iannelli, Fabio, Radaelli, Enrico, Dos Santos, Alexandre, Rapoud, Delphine, Guettier, Catherine, Samuel, Didier, Natoli, Gioacchino, Carninci, Piero, Ciccarelli, Francesca D., Luis Garcia-Perez, Jose, Faivre, Jamila and Faulkner, Geoffrey J. (2013). Endogenous retrotransposition activates oncogenic pathways in hepatocellular carcinoma. Cell, 153 (1), 101-111. doi: 10.1016/j.cell.2013.02.032 |
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2013 Journal Article The role of transposable elements in health and diseases of the central nervous systemReilly, Matthew T., Faulkner, Geoffrey J., Dubnau, Joshua, Ponomarev, Igor and Gage, Fred H. (2013). The role of transposable elements in health and diseases of the central nervous system. Journal of Neuroscience, 33 (45), 17577-17586. doi: 10.1523/JNEUROSCI.3369-13.2013 |
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2012 Journal Article Extensive somatic L1 retrotransposition in colorectal tumorsSolyom, 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 |
