Computational and molecular biology

To understand the roles played by retrotransposons in early mammalian embryogenesis, and in neurons

Professor Faulkner’s research seeks to understand the role of retrotransposons, a type of “mobile DNA”, in causing genetic mosaicism in early mammalian embryogenesis, and in neurons.

This variation may be a fundamental aspect of healthy brain function, and appears to change in neurological diseases, including Rett syndrome, schizophrenia and Alzheimer's disease.

Professor Faulkner published a landmark work in Nature describing somatic retrotransposition in the human brain that was selected by the US National Institute of Mental Health as the 'joint No. 1 research advance of 2011' and has followed this work with four breakthrough articles in Cell and Molecular Cell. He is the recipient of the ASMR Queensland Premier’s Award (2009), the FEBS Anniversary Prize (2011), the Lorne Genome Millennium Science Award (2014), the Centenary Institute Lawrence Creative Prize (2014) and the Australian Academy of Science Ruth Stephens Gani Medal (2016).

Group leader

 Professor Geoff Faulkner

Professor Geoff Faulkner

Group Leader, Computational and molecular biology

Professor, Neuroscience Queensland Brain Institute

  +61 7 334 66300
  g.faulkner@uq.edu.au
  UQ Researcher Profile

Better understand how the genome - our “book of life” - changes in normal and diseased brain cells.

QBI Professor awarded $1.25 million CSL Centenary Fellowship

  • Nanopore sequencing enables comprehensive transposable element epigenomic profiling

    Ewing, Adam D., Smits, Nathan, Sanchez-Luque, Francisco J., Faivre, Jamila, Brennan, Paul M., Richardson, Sandra R., Cheetham, Seth W. and Faulkner, Geoffrey J. (2020). Nanopore sequencing enables comprehensive transposable element epigenomic profiling. Molecular Cell, 80 (5), 915-928.e5. doi: 10.1016/j.molcel.2020.10.024

  • 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

  • L1 mosaicism in mammals: extent, effects, and evolution

    Faulkner, Geoffrey J. and Garcia-Perez, Jose L. (2017). L1 mosaicism in mammals: extent, effects, and evolution. Trends in Genetics, 33 (11), 802-816. doi: 10.1016/j.tig.2017.07.004

  • 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 1-14. doi:10.1038/ncomms10286

  • 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. Cell161 2: 228-239. doi:10.1016/j.cell.2015.03.026

  • 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 Genetics48 1-27. doi:10.1146/annurev-genet-120213-092412

  • 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. Cell153 1: 101-111. doi:10.1016/j.cell.2013.02.032

  • Somatic retrotransposition alters the genetic landscape of the human brain

    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. Nature479 7374: 534-537. doi:10.1038/nature10531

  • The regulated retrotransposon transcriptome of mammalian cells

    Faulkner, Geoffrey J., Kimura, Yasumasa, Daub, Carsten O., Wani, Shivangi, Plessy, Charles, Irvine, Katharine M., Schroder, Kate, Cloonan, Nicole, Steptoe, Anita L., Lassmann, Timo, Waki, Kazunori, Hornig, Nadine, Arakawa, Takahiro, Takahashi, Hazuki, Kawai, Jun, Forrest, Alistair R. R., Suzuki, Harukazu, Hayashizaki, Yoshihide, Hume, David A., Orlando, Valerio, Grimmond, Sean M. and Carninci, Piero (2009) The regulated retrotransposon transcriptome of mammalian cells. Nature genetics41 5: 563-571. doi:10.1038/ng.368

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Research areas

  • Retrotransposons
  • Genetic mosaicism
  • Rett sydnrome, schizophrenia, & Alzheimer's disease

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