Dr Jimmy Breen

Dr Jimmy Breen
 Org Unit Robinson Research Institute
 Email jimmy.breen@adelaide.edu.au
 Telephone +61 8 8313 9228
 Location Floor/Room WS6071.04 ,  Adelaide Health and Medical Sciences ,   North Terrace
  • Biography/ Background

    I am a the head of the Bioinformatics facility at the Robinson Research Institute and member of the University of Adelaide's Bioinformatics Hub. My expertise is primarily in next-generation sequencing and genomics research. I have over 10 years experience dealing with data in a wide variety of fields such as cereal genomics, ancient DNA, evolutionary biology, metagenomics and epigenetics. I am also a lecturer in Bioinformatics in the Faculty of Sciences's Master of Biotechnology course. I was previously a Bioinformatician and genomics researcher at the Australian Centre for Ancient DNA and the School of Agriculture, Food and Wine.

    As a PhD candidate I researched genome assembly strategies in organisms with complex genome structures such as bread wheat. Wheat has a allo-hexaploid genome structure, over 90% repetitive sequence and is over 17 billion pairs (5x larger than the human genome). As a postdoctoral researcher at the University of Zurich, Switzerland I aimed to reduce complexity within a chromosome arm by producing a physical map of chromosome 1AS as part of the European Union's 7th framework project 'Triticeae Genome' (http://www.triticeaegenome.eu).

    My last postdoctoral research project investigated ancient DNA and the analysis of plant remains uncovered by archaeologists in Armenia. Areni-1 is a cave located south-east of the Armenian captial of Yeveran and contains a large array of well-preserved plant samples from as far back as the Chalcolithic (8,000-5,100 years ago). The cave has uncovered some interesting artefacts including the world's oldest shoe and the earlist known winery

    My research interests are in epigenetics, medical genomics and next-generation sequencing applications, working with biomedical researchers located within the Robinson Research Institute. I also have extensive experience in open-access data projects, leading the development of an open-access genomic data repository called the Online Ancient Genome Repository (OAGR).


    For additional information about me, please visit my githubIO site


    Postdoctoral employment

    2006 - 2009 PhD Candidate (Bioinformatics) Centre for Comparative Genomics, Murdoch University

    2009 - 2012 Postdoctoral Research Fellow Institute for Plant Biology, University of Zurich, Switzerland.

    2012 - 2013 Bioinformatics Officer Australian Genome Research Facility, Brisbane, Australia

    2013 - 2016 Postdoctoral Research Fellow Australian Centre for Ancient DNA/School of Agriculture, Food and Wine, University of Adelaide

    2016 - Current Head, Bioinformatics Robinson Research Institute, University of Adelaide



    Memberships and Awards

    2015 Inaugral committee member and communications officer of the Epigenetics Consortium of South Australia (EpiCSA) 

    2010 - present Member of the International Wheat Genome Sequencing Consortium (IWGSC)

    2010 IWGSC PAG Workshop Early Career Speaker travel award


  • Qualifications

    2009 PhD in Bioinformatics

    Murdoch University, Western Australia

    Doctoral thesis titled 'Assembly of a Complex Genome: Defining Elements of Structure and Function'


    2006 Bachelor of Science (honours) majoring in Molecular Biology

    Murdoch University, Western Australia

    Honours thesis titled 'Characterising biological features contained in a novel wheat BAC clone using comparative genomics and bioinformatics'


  • Research Funding


    2015-2016 Partner Investigator

    AGRF Pilot program in Genomics for Agriculture and Environmental Sectors

    Dr Cassandra Collins; Dr Carlos Marcelino RodriguezLopez; Dr Roberta De Bei; Dr Jimmy Breen; Associate Prof. Timothy Cavagnaro; Associate Prof. Matthew Gilliham; Associate Prof. Andrew Metcalfe

    The eco-genomics of wine terroir


    2013-2015 Partner Investigator

    ARC Discovery Grant (DP130104227)

    Prof Michael J Wilkinson; Dr James M Breen; Dr Thomas F Higham; Dr Ron Pinhasi

    Reconstructing wheat evolution using ancient DNA


    2014-2016 Collaborator

    ARC Linkage Grant (LP130100648)

    Prof Alan Cooper, Prof Michael Wilkinson, Dr Matthew Gilliham, Dr John Stephen, A/Prof David Salt, Prof Ron Pinhasi, Prof Thomas Higham, Mr Daniel Densham

    Identifying the diversity and evolution of loci associated with adaptation to aridity/heat and salinity in ancient cereal crops



    2013-2014 Partner Investigator

    Waite Research Institute Platform Technologies

    Dr. Cassandra Collins; Dr. Roberta De Bei; Dr. Carlos Marcelino Rodriguez Lopez; Dr. James Breen

    We prefer them old: Epigenetic control of wine quality in response to grapevine age


    2013-2014 Partner Investigator

    University of Adelaide Interdisciplinary Research Funding (IRF)

    Dr. Iain Searle; Dr. Cassandra Collins; Dr. Carlos Marcelino Rodriguez Lopez; Dr. James Breen

    RNA directed epigenetics in grapevines- a paradigm sh¡ft for plant and animal breeding


  • Publications

    For publications look at my Google Scholar Profile:


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Entry last updated: Thursday, 9 Aug 2018

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