Jimmy Breen

Jimmy Breen

Adelaide Medical School

Faculty of Health and Medical Sciences

Eligible to supervise Masters and PhD - email supervisor to discuss availability.


I am a Bioinformatician/Computational Biologist at the University of Adelaide with experience in plant genomics, ancient DNA, epigenetics and next-generation sequencing (NGS) analysis. I am currently lead the Bioinformatics Core team at the South Australian Health & Medical Research Institute (SAHMRI) and am group leader in Computational Biology at the Robinson Research Institute. I am also co-lecturer of the Master's level Bioinformatics unit (7005 - Bioinformatics and System Modelling) in the MSc Biotechnology course offered at the University of Adelaide.

My research aims to develop computational tools and methods to study the human genome and other model systems. I have a strong emphasis on identifying basic biological insights that can translate to diagnostic applications. My team works on a number of major projects and datasets, including;

- Studying the placental genome and identifying biomarkers to monitor placental abnormalities during pregnancy (led by Professor Claire Roberts at the Robinson Research Institute). This work is funded by the National Institute of Health (NIH), USA
- Clinical sequencing of Acute Lymphoblastic Leukemia patients for clinical treatment selection (led by SAHMRI Director of Cancer Research Professor Deborah White), as part of the Cancer Flagship project of the Australian Genome Health Alliance.
- Using multi-omics approaches to identifying candidate genes for Cerebral Palsy (led by Professor Jozef Gecz at the Robinson Research Institute), a project developed in part from an International Cerebral Palsy Genomics Consortium (ICPGC) collaboration.
- Identifying how 3D chromosome structure impacts gene regulation in immune system function. This work is led by Associate Professor Simon Barry at the Robinson Research Institute and is funded by an NHMRC Project grant.
- Genome-wide association scan of ~2,000 glaucoma patients. This work is led by Professor Jamie Craig at Flinders University.

Available Research Projects

My research aims to develop computational tools and methods to study the human genome and other model systems. I have a strong emphasis on identifying basic biological insights that can translate to diagnostic applications. My team works on a number of major projects and datasets, including;

  • Studying the placental genome and identifying biomarkers to monitor placental abnormalities during pregnancy (led by Professor Claire Roberts at the Robinson Research Institute). This work is funded by the National Institute of Health (NIH), USA
  • Clinical sequencing of Acute Lymphoblastic Leukemia patients for clinical treatment selection (led by SAHMRI Director of Cancer Research Professor Deborah White), as part of the Cancer Flagship project of the Australian Genome Health Alliance.
  • Using multi-omics approaches to identifying candidate genes for Cerebral Palsy (led by Professor Jozef Gecz at the Robinson Research Institute), a project developed in part from an International Cerebral Palsy Genomics Consortium (ICPGC) collaboration.
  • Identifying how 3D chromosome structure impacts gene regulation in immune system function. This work is led by Associate Professor Simon Barry at the Robinson Research Institute and is funded by an NHMRC Project grant.
  • Genome-wide association scan of ~2,000 glaucoma patients. This work is led by Professor Jamie Craig at Flinders University.
  • Appointments

    Date Position Institution name
    2018 - ongoing Bioinformatics Core Team Leader South Australian Health & Medical Research Institute (SAHMRI)
    2018 - ongoing Research Leader in Computational Biology University of Adelaide
    2016 - ongoing Senior Lecturer University of Adelaide
    2016 - 2018 Bioinformatics Core Facility Manager University of Adelaide
    2013 - 2016 Senior Research Associate University of Adelaide
    2012 - 2013 Bioinformatics Officer Australian Genome Research Facility (AGRF)
    2009 - 2012 Postdoctoral Research Associate University of Zurich
  • Education

    Date Institution name Country Title
    2006 - 2009 Murdoch University Australia PhD
    2000 - 2005 Murdoch University Australia BSc (honours)
  • Research Interests

  • Mark Hutchinson, Kim Hemsley, Nicholas Smith, Kristina Elvidge, Cedric Bardy, Jimmy Breen. Medical Research Future Fund (MRFF). ““Brain in a dish” – Development of a personalised medicine approach for Australian children”, $2,490,949 for 3 years

  • D. Parsons, M. Donnelley, M. Kitchen, K. Morgan, G. Zosky, J. Breen, USA CF Foundation Grant. “Lentiviral CFTR gene-addition in CF rat lungs: Effect of PA infection, safety and efficacy”, $282,491 for 2 years

  • Alastair MacLennan, Jozef Gecz, Mark Corbett, Clare van Eyk, James Breen, Christopher Barnett, S MacLennan, J Rice, R Russo. ORG3921: Cerebral Palsy Foundation Research Grant. “The genetic origins of cerebral palsy”. 4 years

  • Sarah Robertson, John Schjenken, Emilie Rissman, Lachlan Moldenhauer & James Breen. 2018 Channel 7 CRF - Research Grant. “Impact of Phthalate exposure in fathers on programming of offspring neurological phenotype”. 2 years

  • Kate Sanders, Bruno Fonseca Simoes, James Breen (CI), David Hunt, Belinda Chang, Davide Pisani, Mark Hutchinson, Emma Teeling. 2018 ARC Discovery Grant (DP180101688) Cat. 1 Funding. “How are visual gene pathways lost and restored during reptile evolution?”

  • Simon Barry, Marc Beyer, Alistair Forrest, Joachim Schultze, Jennifer Couper, James Breen (CIF). 2017 NHRMC Project Grant (APP1120543) Cat. 1 Funding. “Identification of the conformation dependant targets of autoimmune disease linked variation in human regulatory T-cells”

  • Claire Roberts, Tina Bianco-Miotto, Gus Dekker & James Breen (Co-I). 2017 NIH/NIHCD Project Grant (R01): Using Omics to Define Human Placental Development and Function Across Pregnancy. “Maternal molecular profiles reflect placental function and development across gestation”

  • MSc Bioinformatics (2020)
  • MSc Biotechnology (2016-2020)
  • Current Higher Degree by Research Supervision (University of Adelaide)

    Date Role Research Topic Program Degree Type Student Load Student Name
    2024 Co-Supervisor Clinical Transcriptomic Sequencing Analysis Workflows for Acute Lymphoblastic Leukaemia (ALL): Improving Subtype Characterisation in Complex Fusion Events Doctor of Philosophy Doctorate Full Time Miss Ashlee Jean Thomson
  • Past Higher Degree by Research Supervision (University of Adelaide)

    Date Role Research Topic Program Degree Type Student Load Student Name
    2020 - 2023 Co-Supervisor Evolutionary Genomics of an Adaptive Radiation: Viviparous Sea Snakes (Elapidae) Doctor of Philosophy Doctorate Full Time Mr Alastair John Ludington
    2019 - 2023 Principal Supervisor Bioinformatic approaches to variant detection and subtype classification in acute lymphoblastic leukaemia Doctor of Philosophy Doctorate Full Time Miss Jacqueline Ann Rehn
    2018 - 2022 Principal Supervisor Monitoring Placental Development and Function in the Age of Multi-Omic High Throughput Sequencing Doctor of Philosophy Doctorate Full Time Ms Melanie Denise Smith
    2018 - 2020 Co-Supervisor The Molecular Mechanism of Progesterone Receptor in Regulating Gene Expression in Mouse Granulosa Cells during Ovulation Doctor of Philosophy Doctorate Full Time Dr Doan Thao Dinh
    2017 - 2020 Co-Supervisor Epigenetic Profiling of Human Placenta Throughout Early Gestation Doctor of Philosophy Doctorate Full Time Ms Qianhui Wan
    2017 - 2021 Co-Supervisor Development and application of genomic approaches for resolving complex traits among insect pests Doctor of Philosophy Doctorate Full Time Mr Christopher Michael Ward
    2017 - 2021 Principal Supervisor Three-dimensional regulation: Establishing novel linkages between non-coding genetic variation and target genes Doctor of Philosophy Doctorate Full Time Mr Ning Liu
    2015 - 2018 Co-Supervisor Omic Characterisation of Placental Development and Phenotype Doctor of Philosophy Doctorate Full Time Mr Benjamin Thomas Mayne
    2015 - 2019 Co-Supervisor Ancient Plant DNA to the Rescue: Unlocking Crop Genetic Diversity from the Past Doctor of Philosophy Doctorate Full Time Mr Oscar Andres Estrada Santamaria
    2014 - 2017 Co-Supervisor Climate-Driven Ecological Changes Through the Last Glacial Period: Innovations in Plant Ancient DNA and Stable Isotope Palaeoecology Doctor of Philosophy Doctorate Full Time Mr Tim Rabanus-Wallace

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