Bioinfo:RAdelaide

Curriculum Vitae

Dr James (Jimmy) Breen
Bioinformatics & Genomics Researcher

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Professional Associations & Committees

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

Dinh DT, Breen J, Akison LK, DeMayo FJ, Brown HM, Robker RL & Russell DL. Characterization of progesterone receptor-chromatin binding properties and tissue-specific gene expression in mouse reproductive tissues. Submitted

Weyrich L, Farrer A, EisenhoferR, Arriola LA, YoungJ, Selway C, Handsley-Davis M, Adler CJ, Breen J & Cooper A. Laboratory contamination over time during low-biomass sample analysis. Molecular Ecology Resources. In Review

Kedzior SGE, Bianco-Miotto T, Breen J, Diener KR, Donnelley M, Dunning KR, Penno MAS, Rumbold AR, Schjenken JE, Sharkey DJ, Hodyl NA, Fullston T, Gardiner M & Brown HM. It takes a community to conceive: Availability and accuracy of online resources for couples trying to conceive. In Review

Lim M, Kind KL, Breen J, Anastasi MR, Ritter LJ, Tregoweth E, Dinh D, Thompson JG & Brown HM. Hemoglobin expression in in vivo murine preimplantation embryos suggests a role in oxygen-regulated gene expression. In Review

Estrada O, Breen J, Richards SM and Cooper, A. (2018). From seeds to sequence: Ancient plant DNA in the genomic era. Nature Plants. Accepted 22/05/2018. Corresponding/Senior Author

MacLennan A, Kruer M, Baynam G, Moreno-De-Luca A, Wilson Y, Zhu C, Wintle R, Gecz, J, On behalf of the members of the International Cerebral Palsy Genomics Consortium. (2018). Cerebral palsy and genomics: an international consortium. Developmental Medicine and Child Neurology. 60(2), 209-210. doi:10.1111/dmcn.13643

Sadlon T, Brown CY, Bandara V, Hope CM, Schjenken J, Pederson S, Breen J, Forrest A, Beyer M, Robertson SA and Barry SC. (2018), Unravelling the molecular basis for regulatory T cell plasticity. Clinical & Translational Immunology, Accepted 30/01/2018

Mayne BT, Leemaqz S, Buckberry S, Rodriguez Lopez CM, Roberts CT, Bianco-Miotto T & Breen J. (2018). msgbsR: an R package for analysing methylation-sensitive restriction enzyme sequencing data. Scientific Reports. Accepted 03/01/2018 Corresponding/Senior Author

Breen J, Mur LAJ, Sivakumaran A, Akinyemi A, Wilkinson MJ & Rodriguez Lopez CM. (2017). 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

Xie H, Konate M, Sai N, Tesfamicael KG, Cavagnaro T, Gilliham T, Breen J, Metcalfe A, Stephen JR, DeBei R, Collins C & Rodriguez Lopez CM. (2017). Global DNA methylation patterns can play a role in defining terroir in grapevine (Vitis vinifera cv. Shiraz). Frontiers in Plant Science. Accepted 12/10/2017
Preprint: bioRxiv https://www.biorxiv.org/content/early/2017/04/29/127977

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. 68(7): 1519-1529. doi:10.1093/jxb/erx051

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. 0125 doi:10.1038/s41559-017-0125

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. 544, 357–361 (20 April 2017) doi:10.1038/nature21674
Data: doi:10.4225/55/584775546a409

Mayne BT, Leemaqz SY, Smith AK, Breen J, Roberts CT & Bianco-Miotto T. (2017). Accelerated placental aging in early onset preeclampsia pregnancies identified by DNA methylation Epigenomics. 9(3):279-289 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

Conference Proceeding

Wilkinson MJ, Ronca S, Clare A, Riley MC, Young MJ, Warren J, Ford CS & Breen J. (2017). Characterizing difference in pollen carriage by bumblebee species in unimproved pastures. Grassland resources for extensive farming systems in marginal lands: major drivers and future scenarios. Proceedings of the 19th Symposium of the European Grassland Federation. Alghero, Italy, 7-10 May 2017. Pages 633-635 https://www.cabdirect.org/cabdirect/abstract/20173250776

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 (as presenting author)

Mayne Benjamin T, Leemaqz S, Buckberry S, Rodriguez Lopez CM, Roberts CT, Bianco-Miotto T & Breen J. (2017). msgbsR: an R package for analysing methylation-sensitive genotyping-by-sequencing data Genotyping-by-sequencing (GBS). BioC2017: BioC 2017: Where Software and Biology Connect Boston, USA. Poster

Breen J, Rodriguez Lopez CM, De Bei R, David R, Searle I & Collins C. (2016). Whole methylome analysis of grapevine (Vitis vinifera) reveals tissue specific DNA methylation variation. Australian Bioinformatics and Computational Biology Society (ABACBS) Annual Research Meeting 2016. November 2016. Presentation

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. Poster

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

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

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. Presentation

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

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. Poster

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

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. Presentation

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. Presentation

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. Presentation

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