Dr Jimmy Breen
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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
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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'
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Research Funding
Current
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
Completed
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
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Publications
For publications look at my Google Scholar Profile:
https://scholar.google.com/citations?user=gYMeouMAAAAJ&hl=en
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Entry last updated: Monday, 4 Jan 2016