Professor

Geoff Faulkner

Email: 
Phone: 
+61 7 334 66300

Availability

Professor Geoff Faulkner is:
Available for supervision

Qualifications

  • Bachelor (Honours) of Science (Advanced), The University of Queensland
  • Doctor of Philosophy, The University of Queensland

Search Professor Geoff Faulkner’s works on UQ eSpace

107 works between 2003 and 2025
All (107) Journal Article (92) Book Chapter (6) Conference Publication (7) Other Outputs (2)

21 - 40 of 107 works

2022

Journal Article

Somatic retrotransposition in the developing rhesus macaque brain

Billon, Victor, Sanchez-Luque, Francisco J, Rasmussen, Jay, Bodea, Gabriela O, Gerhardt, Daniel J, Gerdes, Patricia, Cheetham, Seth W, Schauer, Stephanie N, Ajjikuttira, Prabha, Meyer, Thomas J, Layman, Cora E, Nevonen, Kimberly A, Jansz, Natasha, Garcia-Perez, Jose L, Richardson, Sandra R, Ewing, Adam D, Carbone, Lucia and Faulkner, Geoffrey J (2022). Somatic retrotransposition in the developing rhesus macaque brain. Genome Research, 32 (7), gr.276451.121-1314. doi: 10.1101/gr.276451.121

Somatic retrotransposition in the developing rhesus macaque brain

2022

Journal Article

HUSH, retrotransposon RNA, you're NEXT to decay

Faulkner, Geoffrey J. (2022). HUSH, retrotransposon RNA, you're NEXT to decay. Molecular Cell, 82 (9), 1610-1612. doi: 10.1016/j.molcel.2022.04.013

HUSH, retrotransposon RNA, you're NEXT to decay

2022

Journal Article

Retrotransposons: still mobile in humans

Faulkner, Geoffrey J. (2022). Retrotransposons: still mobile in humans. Nature Reviews Genetics, 23 (8), 458-459. doi: 10.1038/s41576-022-00485-6

Retrotransposons: still mobile in humans

2022

Journal Article

LINE-1 retrotransposon activation intrinsic to interneuron development

Bodea, Gabriela O., Ferreiro, Maria E., Sanchez-Luque, Francisco J., Botto, Juan M., Rasmussen, Jay, Rahman, Muhammed A., Fenlon, Laura R., Gubert, Carolina, Gerdes, Patricia, Bodea, Liviu-Gabriel, Ajjikuttira, Prabha, Kozulin, Peter, Billon, Victor, Morell, Santiago, Kempen, Marie-Jeanne H.C., Love, Chloe J., Palmer, Lucy M., Ewing, Adam D., Jhaveri, Dhanisha J., Richardson, Sandra R., Hannan, Anthony J. and Faulkner, Geoffrey J. (2022). LINE-1 retrotransposon activation intrinsic to interneuron development.

LINE-1 retrotransposon activation intrinsic to interneuron development

2022

Book Chapter

Locus-specific DNA methylation profiling of human LINE-1 retrotransposons

Sanchez-Luque, Francisco J., Kempen, Marie-Jeanne H. C. and Faulkner, Geoffrey J. (2022). Locus-specific DNA methylation profiling of human LINE-1 retrotransposons. Genomic structural variants in nervous system disorders. (pp. 197-227) edited by Christos Proukakis. New York, NY, United States: Humana Press. doi: 10.1007/978-1-0716-2357-2_11

Locus-specific DNA methylation profiling of human LINE-1 retrotransposons

2021

Journal Article

The evolving gene regulatory landscape—a tinkerer of complex creatures

Faulkner, Geoffrey J. (2021). The evolving gene regulatory landscape—a tinkerer of complex creatures. Genome Biology, 22 (1) 199, 199. doi: 10.1186/s13059-021-02412-0

The evolving gene regulatory landscape—a tinkerer of complex creatures

2021

Journal Article

Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network

Grapotte, Mathys, Saraswat, Manu, Bessière, Chloé, Menichelli, Christophe, Ramilowski, Jordan A., Severin, Jessica, Hayashizaki, Yoshihide, Itoh, Masayoshi, Tagami, Michihira, Murata, Mitsuyoshi, Kojima-Ishiyama, Miki, Noma, Shohei, Noguchi, Shuhei, Kasukawa, Takeya, Hasegawa, Akira, Suzuki, Harukazu, Nishiyori-Sueki, Hiromi, Frith, Martin C., Abugessaisa, Imad, Aitken, Stuart, Aken, Bronwen L., Alam, Intikhab, Alam, Tanvir, Alasiri, Rami, Alhendi, Ahmad M. N., Alinejad-Rokny, Hamid, Alvarez, Mariano J., Andersson, Robin, Arakawa, Takahiro ... Lecellier, Charles-Henri (2021). Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network. Nature Communications, 12 (1) 3297. doi: 10.1038/s41467-021-23143-7

Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network

2021

Journal Article

Hcv activates somatic l1 retrotransposition—a potential hepatocarcinogenesis pathway

Sudhindar, Praveen D., Wainwright, Daniel, Saha, Santu, Howarth, Rachel, McCain, Misti, Bury, Yvonne, Saha, Sweta S., McPherson, Stuart, Reeves, Helen, Patel, Arvind H., Faulkner, Geoffrey J., Lunec, John and Shukla, Ruchi (2021). Hcv activates somatic l1 retrotransposition—a potential hepatocarcinogenesis pathway. Cancers, 13 (20) 5079, 5079. doi: 10.3390/cancers13205079

Hcv activates somatic l1 retrotransposition—a potential hepatocarcinogenesis pathway

2021

Journal Article

Processed pseudogenes: a substrate for evolutionary innovation. Retrotransposition contributes to genome evolution by propagating pseudogene sequences with rich regulatory potential throughout the genome

Troskie, Robin-Lee, Faulkner, Geoffrey J. and Cheetham, Seth W. (2021). Processed pseudogenes: a substrate for evolutionary innovation. Retrotransposition contributes to genome evolution by propagating pseudogene sequences with rich regulatory potential throughout the genome. BioEssays, 43 (11) 2100186, 2100186. doi: 10.1002/bies.202100186

Processed pseudogenes: a substrate for evolutionary innovation. Retrotransposition contributes to genome evolution by propagating pseudogene sequences with rich regulatory potential throughout the genome

2021

Journal Article

An early proinflammatory transcriptional response to tau pathology is age‐specific and foreshadows reduced tau burden

Rasmussen, Jay, Ewing, Adam D., Bodea, Liviu‐Gabriel, Bodea, Gabriela O., Gearing, Marla and Faulkner, Geoffrey J. (2021). An early proinflammatory transcriptional response to tau pathology is age‐specific and foreshadows reduced tau burden. Brain Pathology, 32 (3) e13018, e13018. doi: 10.1111/bpa.13018

An early proinflammatory transcriptional response to tau pathology is age‐specific and foreshadows reduced tau burden

2021

Journal Article

No evidence of human genome integration of SARS-CoV-2 found by long-read DNA sequencing

Smits, Nathan, Rasmussen, Jay, Bodea, Gabriela O., Amarilla, Alberto A., Gerdes, Patricia, Sanchez-Luque, Francisco J., Ajjikuttira, Prabha, Modhiran, Naphak, Liang, Benjamin, Faivre, Jamila, Deveson, Ira W., Khromykh, Alexander A., Watterson, Daniel, Ewing, Adam D. and Faulkner, Geoffrey J. (2021). No evidence of human genome integration of SARS-CoV-2 found by long-read DNA sequencing. Cell Reports, 36 (7) 109530, 109530. doi: 10.1016/j.celrep.2021.109530

No evidence of human genome integration of SARS-CoV-2 found by long-read DNA sequencing

2021

Journal Article

Hippocampal neurogenesis mediates sex-specific effects of social isolation and exercise on fear extinction in adolescence

Drummond, Katherine D., Waring, Michelle L., Faulkner, Geoffrey J., Blewitt, Marnie E., Perry, Christina J. and Kim, Jee Hyun (2021). Hippocampal neurogenesis mediates sex-specific effects of social isolation and exercise on fear extinction in adolescence. Neurobiology of Stress, 15 100367, 1-16. doi: 10.1016/j.ynstr.2021.100367

Hippocampal neurogenesis mediates sex-specific effects of social isolation and exercise on fear extinction in adolescence

2021

Journal Article

Absence of coding somatic single nucleotide variants within well-known candidate genes in late-onset sporadic Alzheimer's Disease based on the analysis of multi-omics data

Min, Shishi, Li, Zongchang, Shieh, Annie, Giase, Gina, Bao, Riyue, Zhang, Chunling, Kuney, Liz, Kopp, Richard, Asif, Huma, Alliey-Rodriguez, Ney, Qin, Lixia, Craig, David Wesley, Faulkner, Geoffrey J., Gershon, Elliot S., Tang, Beisha, Chen, Chao and Liu, Chunyu (2021). Absence of coding somatic single nucleotide variants within well-known candidate genes in late-onset sporadic Alzheimer's Disease based on the analysis of multi-omics data. Neurobiology of Aging, 108, 207-209. doi: 10.1016/j.neurobiolaging.2021.07.010

Absence of coding somatic single nucleotide variants within well-known candidate genes in late-onset sporadic Alzheimer's Disease based on the analysis of multi-omics data

2021

Other Outputs

No evidence of human genome integration of SARS-CoV-2 found by long-read DNA sequencing

Smits, Nathan, Rasmussen, Jay, Bodea, Gabriela O., Amarilla, Alberto A., Gerdes, Patricia, Sanchez-Luque, Francisco J., Ajjikuttira, Prabha, Modhiran, Naphak, Liang, Benjamin, Faivre, Jamila, Deveson, Ira W., Khromykh, Alexander A., Watterson, Daniel, Ewing, Adam D. and Faulkner, Geoffrey J. (2021). No evidence of human genome integration of SARS-CoV-2 found by long-read DNA sequencing. doi: 10.1101/2021.05.28.446065

No evidence of human genome integration of SARS-CoV-2 found by long-read DNA sequencing

2021

Journal Article

Long-read cDNA sequencing identifies functional pseudogenes in the human transcriptome

Troskie, Robin-Lee, Jafrani, Yohaann, Mercer, Tim R., Ewing, Adam D., Faulkner, Geoffrey J. and Cheetham, Seth W. (2021). Long-read cDNA sequencing identifies functional pseudogenes in the human transcriptome. Genome Biology, 22 (1) 146, 1-15. doi: 10.1186/s13059-021-02369-0

Long-read cDNA sequencing identifies functional pseudogenes in the human transcriptome

2021

Journal Article

Endogenous retroviruses in the origins and treatment of cancer

Jansz, Natasha and Faulkner, Geoffrey J. (2021). Endogenous retroviruses in the origins and treatment of cancer. Genome Biology, 22 (1) 147, 1-22. doi: 10.1186/s13059-021-02357-4

Endogenous retroviruses in the origins and treatment of cancer

2020

Journal Article

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

Nanopore sequencing enables comprehensive transposable element epigenomic profiling

2020

Conference Publication

Sex-specific effect of early-life social isolation and exercise on the extinction of adolescent conditioned fear

Drummond, Katherine, Waring, Michelle, Blewitt, Marnie, Faulkner, Geoffrey, Perry, Christina and Kim, Jee Hyun (2020). Sex-specific effect of early-life social isolation and exercise on the extinction of adolescent conditioned fear. 75th Annual Scientific Convention and Meeting of the Society-of-Biological-Psychiatry (SOBP), New York, NY, United States, 30 April - 2 May 2020. Philadelphia, PA, United States: Elsevier. doi: 10.1016/j.biopsych.2020.02.866

Sex-specific effect of early-life social isolation and exercise on the extinction of adolescent conditioned fear

2020

Journal Article

Overcoming challenges and dogmas to understand the functions of pseudogenes

Cheetham, Seth W., Faulkner, Geoffrey J. and Dinger, Marcel E. (2020). Overcoming challenges and dogmas to understand the functions of pseudogenes. Nature Reviews Genetics, 21 (3), 191-201. doi: 10.1038/s41576-019-0196-1

Overcoming challenges and dogmas to understand the functions of pseudogenes

2019

Journal Article

Visualization and analysis of RNA-Seq assembly graphs

Nazarie, Fahmi W., Shih, Barbara, Angus, Tim, Barnett, Mark W., Chen, Sz-Hau, Summers, Kim M., Klein, Karsten, Faulkner, Geoffrey J., Saini, Harpreet K., Watson, Mick, Dongen, Stijn van, Enright, Anton J. and Freeman, Tom C. (2019). Visualization and analysis of RNA-Seq assembly graphs. Nucleic Acids Research, 47 (14), 7262-7275. doi: 10.1093/nar/gkz599

Visualization and analysis of RNA-Seq assembly graphs

Current funding

  • 2025 - 2028
    The mobile DNA origins of gene regulation
    ARC Discovery Projects
    Open grant
  • 2025 - 2029
    Mobile DNA decides neuronal fate in the normal and degenerative human brain
    NHMRC Investigator Grants
    Open grant
  • 2023 - 2027
    Using complex models of human trophoblast to study placental biology and disease (NHMRC Synergy grant led by University of Adelaide)
    University of Adelaide
    Open grant

Past funding

  • 2021 - 2024
    Long-read genetic and epigenetic profiling in lung cancer for precision medicine
    Priority-driven Collaborative Cancer Research Scheme
    Open grant
  • 2020 - 2024
    Somatic genome mosaicism in human brain function and neurodegeneration
    NHMRC Investigator Grants
    Open grant
  • 2020 - 2023
    Visualising genetic mosaicism during development
    ARC Discovery Projects
    Open grant
  • 2018 - 2020
    Hyperactive mobile DNA in schizophrenia
    NHMRC Project Grant
    Open grant
  • 2017 - 2019
    Does mobile DNA activity contribute to reproductive failure?
    NHMRC Project Grant
    Open grant
  • 2017 - 2019
    Epigenetic signatures of abnormal adult neurogenesis in Rett syndrome
    NHMRC Project Grant
    Open grant
  • 2017 - 2021
    The functional impact of neuronal L1 retrotransposition in learning and neurodegeneration
    CSL Limited
    Open grant
  • 2017 - 2018
    Unlocking the cellular determinants of retrotransposition
    ARC Discovery Projects
    Open grant
  • 2016 - 2018
    Does mobile DNA impact memory formation?
    NHMRC Project Grant
    Open grant
  • 2016 - 2020
    Neuronal genome mosaicism: a molecular component of cognition?
    NHMRC Research Fellowship
    Open grant
  • 2014 - 2017
    Somatic Mutations in Brain in Alzheimer's Disease (NIH Grant administered by the University of Chicago)
    University of Chicago, The
    Open grant
  • 2014 - 2016
    A three-tiered strategy to prevent destabilisation of the induced pluripotent stem cell genome by L1 retrotransposition
    NHMRC Project Grant
    Open grant
  • 2014 - 2016
    Harnessing endogenous L1-mediated mutagenesis to elucidate new candidate genes for liver cancer
    NHMRC Project Grant
    Open grant
  • 2013 - 2015
    Genetic consequences of mobile DNA activation in abnormal neurodevelopment
    NHMRC Project Grant
    Open grant
  • 2013 - 2015
    Mobile DNA as a contributor to human brain cancer
    NHMRC Project Grant
    Open grant
  • 2013 - 2015
    NHMRC Career Development Fellowship (R.D Wright Biomedical CDF Level1): L1 retrotransposition in human development and disease
    NHMRC Career Development Fellowship
    Open grant
  • 2013 - 2016
    Uncovering the impact of tandem repeat variation on both common and syndromic forms of paediatric obesity
    NHMRC Project Grant
    Open grant

Availability

Professor Geoff Faulkner is:
Available for supervision

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Supervision history

Current supervision

  • Doctor Philosophy

    Understanding LINE-1 retrotransposon activity in healthy and diseased dopaminergic neurons

    Principal Advisor

    Other advisors: Dr Gabriela-Oana Bodea

  • Doctor Philosophy

    Rewiring transcription in solid tumours by targeting transposable elements

    Principal Advisor

  • Doctor Philosophy

    Understanding LINE-1 retrotransposon activity in healthy and diseased dopaminergic neurons

    Principal Advisor

    Other advisors: Dr Gabriela-Oana Bodea

  • Doctor Philosophy

    The transposable element regulatory landscape of implantation and trophoblast differentiation

    Principal Advisor

  • Doctor Philosophy

    L1 retrotransposon regulation in the mammalian neuronal lineage

    Principal Advisor

    Other advisors: Dr Sandra Richardson, Dr Gabriela-Oana Bodea

  • Doctor Philosophy

    Visualising genetic mosaicism during development

    Principal Advisor

    Other advisors: Dr Sandra Richardson, Dr Gabriela-Oana Bodea

  • Doctor Philosophy

    Investigations into genetic aberrations underlying recurrent ovarian cancer

    Associate Advisor

  • Doctor Philosophy

    Developing genomic profiling techniques using synthetic DNA methylases

    Associate Advisor

    Other advisors: Associate Professor Seth Cheetham

  • Doctor Philosophy

    Jumping Genes in Mammalian Development

    Associate Advisor

    Other advisors: Dr Sandra Richardson

Completed supervision

Enquiries

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