Bioinfo:RAdelaide

Curriculum Vitae

Dr James (Jimmy) Breen
Bioinformatics & Genomics Researcher

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Academic & Professional Positions

Current

2016-Current University of Adelaide
Bioinformatics Leader, Robinson Research Institute &
University of Adelaide Bioinformatics Hub
(Adelaide, SA Australia)

2013-16 University of Adelaide
Senior Research Associate
Australian Centre for Ancient DNA (ACAD) &
School of Agriculture, Food and Wine
(Adelaide, SA Australia)

2012-13 Australian Genome Research Facility (AGRF)
Bioinformatics Officer
Brisbane node (Brisbane, QLD Australia)

2009-12 University of Zurich
Postdoctoral Research Associate
Institute of Plant Biology (Zurich, Switzerland)

Education

2006-09 Murdoch University
PhD Bioinformatics
Supervisors: Matthew Bellgard & Rudi Appels

2000-06 Murdoch University
BSc (hons.) Molecular Biology & Bioinformatics (First Class Honours)
Supervisors: Matthew Bellgard & Rudi Appels

Competitive Grants & External Research Funding

Current

Completed

Publications

Tikhomirova A, Standish AJ, Zhou Y, Breen J, Pederson S, Zilm PS & Kidd SP. (2017). Specific growth conditions induce a Streptococcus pneumoniae non-mucoidal, Small Colony Variant and determine the outcome of its interactions in co-culture with Haemophilus influenzae. Frontiers in Cellular and Infection Microbiology In Review

Hyles J, Vautrin S, Pettolino F, Macmillan C, Stachurski Z, Breen J, Berges H, Wicker T & Spielmeyer W. (2017). Repeat length variation in a wheat cellulose synthase-like gene is associated with altered tiller number and stem composition. Journal of Experimental Botany Accepted

Rabanus-Wallace MT, Wooller MJ, Zazula G, Shute E, Jahren H, Breen J, Llamas B & Cooper A. (2017). Megafaunal nitrogen isotopes reveal role of global moisture-driven decline of rangelands in Late Pleistocene extinctions. Nature Ecology & Evolution Accepted

Weyrich LS, Duchene S, Soubrier J, Arriola L, Llamas B, Breen J, Morris AG, Alt KW, Caramelli D, Dresely V, Farrell M, Farrer AG, Francken M, Gully N, Haak W, Hardy K, Harvati K, Held P, Holmes EC, Kaidonis J, Lalueza-Fox C, de la Rasilla M, Rosas A, Semal P, Soltysiak A, Townsend G, Usai D, Wahl J, Huson DH, Dobney K & Cooper A. (2017). Reconstructing Neandertal behavior, diet, and disease using ancient DNA from dental calculus Nature In Press
Data: doi:10.4225/55/584775546a409

Breen J, Mur LAJ, Sivakumaran A, Akinyemi A, Wilkinson MJ & Rodriguez Lopez CM. (2016). Botrytis cinerea loss and restoration of virulence during in vitro culture follows flux in global DNA methylation. In Review
Preprint: bioRxiv http://biorxiv.org/content/early/2016/08/26/059477

Mayne BT, Leemaqz SY, Smith AK, Breen J, Roberts CT & Bianco-Miotto T. (2016). Accelerated placental aging in early onset preeclampsia pregnancies identified by DNA methylation Epigenomics. doi:10.2217/epi-2016-0103

Mayne BT, Bianco-Miotto T, Buckberry S, Breen J, Clifton V, Shoubridge C & Roberts CT. (2016). Large scale gene expression meta-analysis reveals tissue-specific, sex-biased gene expression in humans Frontiers in Genetics. doi:10.3389/fgene.2016.00183

Bianco-Miotto T, Mayne BT, Buckberry S, Breen J, Rodriguez Lopez CM & Roberts CT. (2016). Recent progress towards understanding the role of DNA methylation in human placental development Reproduction 152(1): R23-30. doi:10.1530/REP-16-0014

Czechowski P, Clarke LJ, Breen J, Cooper A & Stevens MI. (2016). Antarctic eukaryotic soil diversity of the Prince Charles Mountains revealed by high-throughput sequencing Soil Biology and Biochemistry 95: 112-121 doi:10.1016/j.soilbio.2015.12.013

Ellison A, Rodríguez López CM, Moran P, Breen J, Swain M, Megias M, Hegarty M, Wilkinson M, Pawluk R & Consuegra S. (2015). Epigenetic regulation of sex-ratios may explain natural variation in self-fertilisation rates. Proceedings of the Royal Society B 282(1819). doi:10.1098/rspb.2015.1900

Hurni S, Scheuermann D, Krattinger SG, Kessel B, Wicker T, Herren G, Fitze MN, Breen J, Presterl T, Ouzunova M & Keller, B. (2015). The maize disease resistance gene Htn1 against northern corn leaf blight encodes a wall-associated receptor-like kinase. Proceedings of the National Academy of Sciences 112(28): 8780-8785. doi:10.1073/pnas.1502522112

Young J, Weyrich LS, Breen J, Macdonald LM & Cooper A. (2015). Predicting the origin of soil evidence: high throughput eukaryote sequencing and MIR spectroscopy applied to a crime scene scenario. Forensic Science International 251:22–31. doi:10.1016/j.forsciint.2015.03.008

Mago R, Tabe L, Vautrin S, Simková H, Kubaláková M, Upadhyaya N, Berges H, Kong XY, Breen J, Dolezel J, Appels R, Ellis J & Spielmeyer W. (2015). Major haplotype divergence including multiple germin-like protein genes, at the wheat Sr2 adult plant stem rust resistance locus. BMC Plant Biology 14:379 doi:10.1186/s12870-014-0379-z

Breen J, Wicker T, Shatalina M, Frenkel Z, Bertin I, Phillippe R, Spielmeyer W, Doležel J, Simková H, Scalabrin S, Vautrin S, Bergès H, International Wheat Genome Sequencing Consortium, Paux E, Fahima T, Korol A, Feuillet C & Keller B. (2013). A Physical Map of the Short Arm of Wheat Chromosome 1A. PLoS ONE 8(11), e80272. doi:10.1371/journal.pone.0080272

Mago R, Tabe L, McIntosh RA, Pretorius Z, Kota K, Paux E, Wicker T, Breen J, Lagudah ES, Ellis JG & Spielmeyer W. (2011). A multiple resistance locus on chromosome arm 3BS in wheat confers resistance to stem rust (Sr2), leaf rust (Lr27) and powdery mildew. Theoretical and Applied Genomics 123(4): 615-23. doi:10.1007/s00122-011-1611-y

Zhang J, Jia J, Breen J & Kong X. (2011). Recent insertion of a 52-kb mitochondrial DNA segment in the wheat lineage. Functional & Integrative Genomics 11 (4), 599-609. 10.1007/s10142-011-0237-0

Parlange F, Oberhaensli F, Breen J, Platzer M, Taudien S, Simkova H, Wicker T, Dolezel J & Keller B. (2011). A major invasion of transposable elements accounts for the large size of the Blumeria graminis f.sp. tritici genome. Functional and Integrative Genomics 11(4): 671-677. doi:10.1007/s10142-011-0240-5

Mago R, Simkova H, Brown-Guedira G, Dreisigacker S, Breen J, Jin Y, Singh R, Appels R, Lagudah ES, Ellis J, Dolezel J & Spielmeyer W. (2011). An accurate DNA marker assay for stem rust resistance gene Sr2 in wheat. Theoretical and Applied Genomics 122(4): 735-44. doi:10.1007/s00122-010-1482-7

Breen, J & Bellgard, M. (2010). Germin-like proteins (GLPs) in cereal genomes: gene clustering and dynamic roles in plant defence. Functional and Integrative Genomics 10(4): 463-76. doi:10.1007/s10142-010-0184-1

Choulet F, Wicker T, Rustenholz, C, Paux, E, Salse, J, Leroy P, Schlub S, LePaslier MC, Magdelenat G, Gonthier C, Couloux A, Budak H, Breen J, Pumphrey M, Liu S, Kong X, Jia J, Gut M, Brunel D, Anderson JA, Gill BS, Appels R, Keller B & Feuillet C. (2010). Megabase level sequencing reveals contrasted organization and evolution patterns of the wheat gene and transposable element spaces. Plant Cell 22(6): 1686-701. doi:10.1105/tpc.110.074187

Breen J, Li D, Dunn DS, Bekes F, Kong X, Zhang J, Jia J, Wicker T, Mago R, Ma W, Bellgard M & Appels R. (2010). Wheat beta-expansin (EXPB11) genes: Identification of the expressed gene on chromosome 3BS carrying a pollen allergen domain. BMC Plant Biology 10: 99. doi:10.1186/1471-2229-10-99

Breen J, Wicker T, Kong X, Zhang J, Ma W, Paux E, Feuillet C, Appels R & Bellgard M. (2010). A highly conserved gene island of three genes on chromosome 3B of hexaploid wheat: diverse gene function and genomic structure maintained in a tightly linked block. BMC Plant Biology 10: 98. doi:10.1186/1471-2229-10-98

Moolhuijzen P, Dunn DS, Bellgard M, Carter M, Jia J, Kong XY, Gill BS, Feuillet C, Breen J, Appels R. (2007). Wheat genome structure and function: genome sequence data and the International Wheat Genome Sequencing Consortium. Crop & Pasture Science 58: 470-75. doi:10.1071/AR06155

Invited Presentations

2015 Building Bioinformatics
Robinson Research Institute, University of Adelaide (Host: Sarah Robertson)
Data: https://bitbucket.org/gammyknee/robinson_talk

2015 Ancient Plants: Adaptation to Climate Change and Domestication
University of Washington, USA (host: Jay Shedure)

2014 Next-generation sequencing of ancient grains from Armenia
University of Swansea, UK (host: Sonia Consuegra)

2009 Sequencing, Assembly and Annotation of large genomic sequences from chromosome 3B, Institut National de la Recherche Agronomique (INRA)
Clermont- Ferrand, France (host: Catherine Feuillet)

2008 Wheat Genome Sequence assembly using Transposable Element Annotation
CSIRO Plant Industries, Canberra, Australia (host: Wolfgang Spielmeyer)

Conference submissions

Breen J, Rabanus-Wallace MT, Pinhasi R, Gasparyan B, Wilkinson MJ & Cooper A. (2015). Ancient DNA analysis of 5,000 year old wheat and barley seeds from Armenia reveal insights into fungal pathogens and wine-making culture in the late chalcolithic. Plant and Animal Genome San Diego, USA

Rodriguez Lopez CM, Breen J, De Bei R, Searle I & Collins C. (2015). We prefer them old: Epigenetic control of wine quality in response to grapevine age. Plant and Animal Genome San Diego, USA

Rodríguez López CM, Ellison A, Moran P, Swain M, Megias M, Hegarty M, Breen J, Wilkinson MJ & Consuegra S. (2015). Can epigenetic regulation of sex-ratios explain natural variation in self-fertilization rates? Plant and Animal Genome San Diego, USA

2013 Breen J, Wilkinson MJ & Cooper A. (2013). Ancient DNA sequencing of late chalcolithic cereal grains from Armenia. Wheat Bioinformatics Forum Adelaide, South Australia

Breen J, Wicker T & Keller B. (2011). Integrating genomic resources and sequencing data of wheat chromosome 1AS. Plant and Animal Genome San Diego, USA

Breen J, Wicker T, Shatalina M & Keller B. (2011). Update on the physical mapping of hexaploid wheat chromosome 1AS. 3rd Triticeae Genome Annual Meeting Prague and Olomouc, Czech Republic

Breen J, Wicker T & Keller B. (2010). Physical Map assembly of chromosome 1AS. 2nd Triticeae Genome Annual Meeting Sabanci University, Istanbul, Turkey

Wicker T, Middleton C & Breen J. (2010). Whole genome surveys of the wheat A, B and D genome donors, rye and barley provides fundamentals for a robust phylogeny of Triticeae. 20th International Triticeae Mapping Initiative & 2nd Wheat Genomics in China Workshop Beijing, China

Breen J, Wicker T, Kong XY, Zhang J, Ma W, Paux E, Feuillet C, Appels R & Bellgard M. (2010). A highly conserved gene island of three genes on chromosome 3B of hexaploid wheat: Diverse gene function and genomic structure maintained in a tightly linked block. 2nd International Symposium on “Genomics of Plant Genetic Resources” Bologna, Italy

Spielmeyer W, Mago R, Simkova H, Dolezel J, Paux E, Feuillet C, Breen J, Appels R, McIntosh R, Raja K, Wellings C & Lagudah E. (2009). Molecular Dissection Of Durable Stem Rust Resistance Gene Locus In Wheat. Plant and Animal Genome San Diego, USA

Spielmeyer W, Mago R, Simkova H, Dolezel J, Krattinger S, Keller B, Paux E, Feuillet C, Breen J, Appels R, McIntosh R, Raja K, Wellings C and Lagudah E. (2009). Durable Rust Resistance In Wheat Is Effective Against Multiple Pathogens. Plant and Animal Genome San Diego, USA

Breen J. (2009). Development of Annotation pipelines based on discussions held internationally during 2007 and 2008. International Wheat Genetics Symposium Brisbane, Australia

Breen J, Appels R & Bellgard M. (2008). Update on chromosome 3B BAC sequencing. Molecular Plant Breeding Co-operative Research Centre (MPB-CRC) Annual Research Meeting Creswick, VIC Australia

Breen J, Appels R & Bellgard M. (2007). Wheat Genome Sequence Assembly. Molecular Plant Breeding Co- operative Research Centre (MPB-CRC) Annual Research Meeting Barossa Valley, SA Australia

Breen J, Appels R & Bellgard M. (2006). Wheat BAC sequencing of chromosome 3B. Molecular Plant Breeding Co-operative Research Centre (MPB-CRC) Annual Research Meeting Fremantle, WA Australia

Non-academic

2015 DNA Database Scope (Channel 10 Children’s Science Show) (Scope Season 3 Episode 073 PAST PRESENT AND FUTURE)

2015 The Sounds of Science: Open Access to Ancient DNA Radio Adelaide (radio.adelaide.edu.au/open-access-to-ancient-human-dna)

2015 Data bank launched for global access to ancient DNA University of Adelaide Media Release (blogs.adelaide.edu.au/environment/2015/06/18/media-release-data-bank-launched-for-global-access-to-ancient-dna-2)

2013 Talking Research: Dr. James Breen. Harvest: Radio Adelaide (radio.adelaide.edu.au/talking-research-dr-james-breen)

Technical skills

Supervision

Current

Completed

Projects

…more to come…

Awards & Associations