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2016

Journal Article

TET enzymes: double agents in the transposable element-host genome conflict

Gerdes, 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

TET enzymes: double agents in the transposable element-host genome conflict

2016

Journal Article

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) 21, 1-14. doi: 10.1186/s13100-016-0076-6

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

2016

Journal Article

Transposable elements in the mammalian embryo: pioneers surviving through stealth and service

Gerdes, 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

Transposable elements in the mammalian embryo: pioneers surviving through stealth and service

2016

Journal Article

Point mutations in Exon 1B of APC Reveal Gastric Adenocarcinoma and Proximal Polyposis of the Stomach as a Familial Adenomatous Polyposis Variant

Li, 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

Point mutations in Exon 1B of APC Reveal Gastric Adenocarcinoma and Proximal Polyposis of the Stomach as a Familial Adenomatous Polyposis Variant

2016

Journal Article

Reprogramming triggers endogenous L1 and Alu retrotransposition in human induced pluripotent stem cells

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

Reprogramming triggers endogenous L1 and Alu retrotransposition in human induced pluripotent stem cells

2016

Book Chapter

Retrotransposon capture sequencing (RC-Seq): a targeted, high-throughput approach to resolve somatic L1 retrotransposition in humans

Sanchez-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

Retrotransposon capture sequencing (RC-Seq): a targeted, high-throughput approach to resolve somatic L1 retrotransposition in humans

2015

Journal Article

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

Ubiquitous L1 mosaicism in hippocampal neurons

2015

Journal Article

Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells

Arner, 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

Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells

2014

Journal Article

L1 retrotransposons and somatic mosaicism in the brain

Richardson, 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

L1 retrotransposons and somatic mosaicism in the brain

2014

Journal Article

Blood from 'junk': the LTR chimeric transcript Pu.2 promotes erythropoiesis

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

Blood from 'junk': the LTR chimeric transcript Pu.2 promotes erythropoiesis

2014

Journal Article

NanoCAGE analysis of the mouse olfactory epithelium identifies the expression of vomeronasal receptors and of proximal LINE elements

Pascarella, 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

NanoCAGE analysis of the mouse olfactory epithelium identifies the expression of vomeronasal receptors and of proximal LINE elements

2014

Journal Article

L1 retrotransposons, cancer stem cells and oncogenesis

Carreira, 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

L1 retrotransposons, cancer stem cells and oncogenesis

2014

Journal Article

A promoter-level mammalian expression atlas

Forest, 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

A promoter-level mammalian expression atlas

2014

Conference Publication

Line-1, a novel biomarker for high-grade serous ovarian carcinoma

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

Line-1, a novel biomarker for high-grade serous ovarian carcinoma

2014

Journal Article

Diversity through duplication: Whole-genome sequencing reveals novel gene retrocopies in the human population

Richardson, 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

Diversity through duplication: Whole-genome sequencing reveals novel gene retrocopies in the human population

2013

Journal Article

Retrotransposon Silencing During Embryogenesis: Dicer Cuts in LINE

Faulkner, Geoffrey J. (2013). Retrotransposon Silencing During Embryogenesis: Dicer Cuts in LINE. PLoS Genetics, 9 (11) e1003944, e1003944. doi: 10.1371/journal.pgen.1003944

Retrotransposon Silencing During Embryogenesis: Dicer Cuts in LINE

2013

Journal Article

Genome-wide methylated CpG island profiles of melanoma cells reveal a melanoma coregulation network

Li, 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

Genome-wide methylated CpG island profiles of melanoma cells reveal a melanoma coregulation network

2013

Journal Article

Endogenous retrotransposition activates oncogenic pathways in hepatocellular carcinoma

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

Endogenous retrotransposition activates oncogenic pathways in hepatocellular carcinoma

2013

Journal Article

The role of transposable elements in health and diseases of the central nervous system

Reilly, 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

The role of transposable elements in health and diseases of the central nervous system

2012

Journal Article

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

Extensive somatic L1 retrotransposition in colorectal tumors