Journal Articles
Jiang, Jiayue-Clara, Rothnagel, Joseph A. and Upton, Kyle R. (2021). Widespread exaptation of L1 transposons for transcription factor binding in breast cancer. International Journal of Molecular Sciences, 22 (11) 5625, 1-21. doi: 10.3390/ijms22115625
Jiang, Jiayue-Clara, Rothnagel, Joseph A. and Upton, Kyle R. (2021). Integrated transcription factor profiling with transcriptome analysis identifies L1PA2 transposons as global regulatory modulators in a breast cancer model. Scientific Reports, 11 (1) 8083, 8083. doi: 10.1038/s41598-021-86395-9
Hulme, Katina D., Karawita, Anjana C., Pegg, Cassandra, Bunte, Myrna J. M., Bielefeldt-Ohmann, Helle, Bloxham, Conor J., Van den Hoecke, Silvie, Setoh, Yin Xiang, Vrancken, Bram, Spronken, Monique, Steele, Lauren E., Verzele, Nathalie A. J., Upton, Kyle R., Khromykh, Alexander A., Chew, Keng Yih, Sukkar, Maria, Phipps, Simon and Short, Kirsty R. (2021). A paucigranulocytic asthma host environment promotes the emergence of virulent influenza viral variants. eLife, 10 e61803, 1-21. doi: 10.7554/elife.61803
Hulme, Katina Dee, Yan, Limin, Marshall, Rebecca J., Bloxham, Conor J., Upton, Kyle R., Hasnain, Sumaira Z., Bielefeldt-Ohmann, Helle, Loh, Zhixuan, Ronacher, Katharina, Chew, Keng Yih , Gallo, Linda A. and Short, Kirsty Renfree (2020). High glucose levels increase influenza-associated damage to the pulmonary epithelial-endothelial barrier. eLife, 9 e56907, 1-20. doi: 10.7554/elife.56907
Pridans, Clare, Raper, Anna, Davis, Gemma M., Alves, Joana, Sauter, Kristin A., Lefevre, Lucas, Regan, Tim, Meek, Stephen, Sutherland, Linda, Thomson, Alison J., Clohisey, Sara, Bush, Stephen J., Rojo, Rocío, Lisowski, Zofia M., Wallace, Robert, Grabert, Kathleen, Upton, Kyle R., Tsai, Yi Ting, Brown, Deborah, Smith, Lee B., Summers, Kim M., Mabbott, Neil A., Piccardo, Pedro, Cheeseman, Michael T., Burdon, Tom and Hume, David A. (2019). Erratum: Pleiotropic impacts of macrophage ands microglial deficiency on development in rats with targeted mutation of the Csf1r locus (Journal of Immunology (2019) 201 (2683-2699) DOI: 10.4049/jimmunol.1701783). Journal of Immunology, 202 (11), 3334-3335. doi: 10.4049/jimmunol.1900420
Jiang, Jiayue-Clara and Upton, Kyle R. (2019). Human transposons are an abundant supply of transcription factor binding sites and promoter activities in breast cancer cell lines. Mobile DNA, 10 (1) 16, 16. doi: 10.1186/s13100-019-0158-3
Klawitter, Sabine, Fuchs, Nina V., Upton, Kyle R., Muñoz-Lopez, Martin, Shukla, Ruchi, Wang, Jichang, Garcia-Cañadas, 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, Balázs, Löwer, Johannes, Wolvetang, Ernst J., Martin, Ulrich, Ivics, Zoltán, Izsvák, Zsuzsanna, Garcia-Perez, Jose L., Faulkner, Geoffrey J. and Schumann, Gerald G. (2018). Erratum to: Reprogramming triggers endogenous L1 and Alu retrotransposition in human induced pluripotent stem cells (Nature Communications, (2016), 7, 1, (10286), 10.1038/ncomms10286). Nature Communications, 9 (1) 5398, 5398. doi: 10.1038/s41467-018-07917-0
Pridans, Clare, Raper, Anna, Davis, Gemma M., Alves, Joana, Sauter, Kristin A., Lefevre, Lucas, Regan, Tim, Meek, Stephen, Sutherland, Linda, Thomson, Alison J., Clohisey, Sara, Bush, Stephen J, Rojo, Rocío, Lisowski, Zofia M., Wallace, Robert, Grabert, Kathleen, Upton, Kyle R., Tsai, Yi Ting, Brown, Deborah, Smith, Lee B., Summers, Kim M., Mabbott, Neil A., Piccardo, Pedro, Cheeseman, Michael T., Burdon, Tom and Hume, David A. (2018). Pleiotropic impacts of macrophage and microglial deficiency on development in rats with targeted mutation of the Csf1r locus. Journal of Immunology, 201 (9), 2683-2699. doi: 10.4049/jimmunol.1701783
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
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
Klawitter, 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
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
Upton, 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
Shukla, 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
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
Upton, Kyle R., Baillie, J. Kenneth and Faulkner, Geoffrey J. (2011). Is somatic retrotransposition a parasitic or symbiotic phenomenon?. Mobile Genetic Elements, 1 (4), 279-282. doi: 10.4161/mge.18422
Baillie, J. Kenneth, Barnett, Mark W., Upton, Kyle R., Gerhardt, Daniel J., Richmond, Todd A., De Sapio, Fioravante, Brennan. Paul M., Rizzu, Patrizia, Smith, Sarah, Fell, Mark, Talbot, Richard T., Gustincich, Stefano, Freeman, Thomas C., Mattick, John S., Hume, David A., Heutink, Peter, Carninci, Piero, Jeddeloh, Jeffrey A. and Faulkner, Geoffrey J. (2011). Somatic retrotransposition alters the genetic landscape of the human brain. Nature, 479 (7374), 534-537. doi: 10.1038/nature10531
Liu, Jun, Sumer, Huseyin, Leung, Jessie, Upton, Kyle, Dottori, Mirella, Pebay, Alice and Verma, Paul J. (2011). Late passage human fibroblasts induced to pluripotency are capable of directed neuronal differentiation. Cell Transplantation, 20 (2), 193-203. doi: 10.3727/096368910X514305
Tat, Pollyanna A., Sumer, Huseyin, Jones, Karen L., Upton, Kyle and Verma, Paul J. (2010). The efficient generation of induced pluripotent stem (iPS) cells from adult mouse adipose tissue-derived and neural stem cells. Cell Transplantation, 19 (5), 525-536. doi: 10.3727/096368910X491374
Sumer, Huseyin, Jones, Karen L., Liu, Jun, Heffernan, Corey, Tat, Pollyanna A., Upton, Kyle R. and Verma, Paul J. (2010). Reprogramming of somatic cells after fusion with induced pluripotent stem cells and nuclear transfer embryonic stem cells. Stem Cells and Development, 19 (2), 239-246. doi: 10.1089/scd.2009.0142
Conference Papers
Jung-Klawitter, S., Fuchs, N. V., Upton, K. R., Froemmrich, A., Miskey, C., Munoz-Lopez, M., Shukla, R., Wang, J., Sebe, A., Merkert, S., Bock, A., Held, U., Menzel, M., Gogol-Doering, A., Haase, A., Izsvak, Z., Ivics, Z., Martin, U., Garcia-Perez, J., Faulkner, G. J. and Schumann, G. G. (2017). Reprogramming triggers mobilisation of endogenous retrotransposons in human induced pluripotent stem cells with genotoxic effects on host gene expression. European-Society-of-Gene-and-Cell-Therapy (ESCGT) Congress, Berlin, Germany, 2017. New Rochelle, NY, United States: Mary Ann Liebert.
Schumann, Gerald, Jung-Klawitter, 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, Gerdes, Patricia, Merkert, Sylvia, Pulgarin, Andres, Bock, Anja, Held, Ulrike, Witthuhn, Anett, Haase, Alexandra, Wolvetang, Ernst J., Martin, Ulrich, Ivics, Zoltan, Izsvak, Zsuzsanna, Garcia-Perez, J. and Faulkner, Geoffrey J. (2016). Reprogramming initiates mobilization of endogenous mutagenic LINE-1, Alu and SVA retrotransposons in human induced pluripotent stem cells with consequences for host gene expression. Frontiers of Retrovirology Conference 2016, Erlangen, Germany, 12 - 14 September 2016. London, United Kingdom: BioMed Central. doi: 10.1186/s12977-016-0294-5
Nguyen, 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
Upton, Kyle R., Pridans, Clare, Meek, Stephen, Sutherland, Linda, Whitelaw, Bruce, Burdon, Tom and Hume, David (2011). Gene targeting of the rat Csf1r locus using homologous recombination in ES cells. 10th Transgenic Technology Meeting (TT2011), Florida, United States, 24-26 October 2011. Dordrecht, Netherlands: Springer Netherlands. doi: 10.1007/s11248-011-9540-8
Upton, K, Vassiliev, I, Kues, W, McConnell, H and Verma, PJ (2006). Isolation of stem-like cells from adult somatic bovine tissue. 7th Samuel A Latt Conference on Stem Cells in the Age of Fluorescence Technology, Queensland Austria, Nov 06-09, 2005. WILEY-LISS.