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.

My Research
Career
Publications
Grants and Funding
Teaching
Supervision
Professional Activities
Contact

Available Research Projects

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

Bioinformatics Epigenetics Genomics

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

Journals

Year	Citation
2023	Buckberry, S., Liu, X., Poppe, D., Tan, J. P., Sun, G., Chen, J., . . . Lister, R. (2023). Transient naive reprogramming corrects hiPS cells functionally and epigenetically. Nature, 620(7975), 863-872. DOI Scopus2 WoS1
2023	Thomson, A. J., Rehn, J. A., Heatley, S. L., Eadie, L. N., Page, E. C., Schutz, C., . . . White, D. L. (2023). Reproducible Bioinformatics Analysis Workflows for Detecting IGH Gene Fusions in B-Cell Acute Lymphoblastic Leukaemia Patients. Cancers, 15(19), 1-13. DOI
2023	Khurana, I., Howard, N. J., Maxwell, S., Du Preez, A., Kaipananickal, H., Breen, J., . . . El-Osta, A. (2023). Circulating epigenomic biomarkers correspond with kidney disease susceptibility in high-risk populations with type 2 diabetes mellitus. Diabetes Research and Clinical Practice, 204, 9 pages. DOI
2023	Chan, H. Y., Tran, H. M., Breen, J., Schjenken, J. E., & Robertson, S. A. (2023). The endometrial transcriptome transition preceding receptivity to embryo implantation in mice. BMC Genomics, 24(1), 1-16. DOI Europe PMC1
2023	Aldersey, J. E., Liu, N., Tearle, R., Low, W. Y., Breen, J., Williams, J. L., & Bottema, C. D. K. (2023). Topologically associating domains in the POLLED region are the same for Angus- and Brahman-specific Hi-C reads from F1 hybrid fetal tissue.. Anim Genet, 54(4), 536-543. DOI
2023	Wong, Y. Y., Harbison, J. E., Hope, C. M., Gundsambuu, B., Brown, K. A., Wong, S. W., . . . Barry, S. C. (2023). Parallel recovery of chromatin accessibility and gene expression dynamics from frozen human regulatory T cells.. Scientific reports, 13(1), 15 pages. DOI Scopus1
2023	Dinh, D. T., Breen, J., Nicol, B., Foot, N. J., Bersten, D. C., Emery, A., . . . Russell, D. L. (2023). Progesterone receptor mediates ovulatory transcription through RUNX transcription factor interactions and chromatin remodelling.. Nucleic Acids Research, 51(12), 5981-5996. DOI Scopus2 Europe PMC1
2023	Eadie, L. N., Rehn, J. A., Breen, J., Osborn, M. P., Jessop, S., Downes, C. E. J., . . . White, D. L. (2023). Case Report: Rare IKZF1 Gene Fusions Identified in Neonate with Congenital KMT2A-Rearranged Acute Lymphoblastic Leukemia. Genes, 14(2), 264-1-264-11. DOI
2023	Smith, M. D., Leemaqz, S. Y., Jankovic-Karasoulos, T., McCullough, D., McAninch, D., Arthurs, A. L., . . . Pillman, K. A. (2023). DraculR: A Web-Based Application for In Silico Haemolysis Detection in High-Throughput microRNA Sequencing Data. Genes, 14(2), 1-10. DOI
2022	Wong, Y., Harbison, J., Hope, C., Gundsambuu, B., Brown, K., Wong, S., . . . Barry, S. (2022). Parallel recovery of chromatin accessibility and gene expression dynamics from frozen human Regulatory T cells. DOI
2022	Souzeau, E., Siggs, O. M., Mullany, S., Schmidt, J. M., Hassall, M. M., Dubowsky, A., . . . Mills, R. A. (2022). Diagnostic yield of candidate genes in an Australian corneal dystrophy cohort. Molecular Genetics and Genomic Medicine, 10(10), 1-15. DOI Scopus2 WoS2 Europe PMC3
2022	Richards, S. M., Li, L., Breen, J., Hovhannisyan, N., Estrada, O., Gasparyan, B., . . . Zhang, H. (2022). Recovery of chloroplast genomes from medieval millet grains excavated from the Areni-1 cave in southern Armenia. Scientific Reports, 12(1), 15164-1-15164-15. DOI Scopus1
2022	Rehn, J., Mayoh, C., Heatley, S. L., McClure, B. J., Eadie, L. N., Schutz, C., . . . White, D. L. (2022). Rascall: Rapid (Ra) screening (Sc) of RNA-seq data for prognostically significant genomic alterations in acute lymphoblastic leukaemia (ALL). PLoS Genetics, 18(10), 1-23. DOI Scopus8 WoS5 Europe PMC6
2022	Lim, C. K., Romeo, O., Chilver, A., Tran, B. M., Flanagan, D., Kirby, E., . . . Beard, M. (2022). Human Liver Organoids as a Patient-derived Model for HBV Infection and Cellular Response. DOI
2022	Mäkinen, V. -P., Rehn, J., Breen, J., Yeung, D., & White, D. (2022). Multi-cohort transcriptomic subtyping of B-cell acute lymphoblastic leukemia. DOI
2022	Bogias, K. J., Pederson, S. M., Leemaqz, S., Smith, M. D., McAninch, D., Jankovic-Karasoulos, T., . . . Roberts, C. T. (2022). Placental Transcription Profiling in 6–23 Weeks’ Gestation Reveals Differential Transcript Usage in Early Development. International Journal of Molecular Sciences, 23(9), 17 pages. DOI Scopus2 WoS3 Europe PMC3
2022	Smith, M., Leemaqz, S., Jankovic-Karasoulos, T., McAninch, D., McCullough, D., Breen, J., . . . Pillman, K. (2022). Haemolysis detection in microRNA-seq from clinical plasma samples. DOI
2022	Okada, T., McIlfatrick, S., Hin, N., Aryamanesh, N., Breen, J., & St John, J. C. (2022). Mitochondrial supplementation of Sus scrofa metaphase II oocytes alters DNA methylation and gene expression profiles of blastocysts. Epigenetics and Chromatin, 15(1), 20 pages. DOI Scopus7 WoS7 Europe PMC4
2022	Mäkinen, V. -P., Rehn, J., Breen, J., Yeung, D., & White, D. L. (2022). Multi-Cohort Transcriptomic Subtyping of B-Cell Acute Lymphoblastic Leukemia. International Journal of Molecular Sciences, 23(9), 1-17. DOI Scopus5 WoS3 Europe PMC4
2022	Dashti, H., Dehzangi, I., Bayati, M., Breen, J., Beheshti, A., Lovell, N., . . . Alinejad-Rokny, H. (2022). Integrative analysis of mutated genes and mutational processes reveals novel mutational biomarkers in colorectal cancer. BMC Bioinformatics, 23(1), 24 pages. DOI Scopus6 WoS6 Europe PMC7
2022	Liu, N., Sadlon, T., Wong, Y. Y., Pederson, S., Breen, J., & Barry, S. C. (2022). 3DFAACTS-SNP: using regulatory T cell-specific epigenomics data to uncover candidate mechanisms of type 1 diabetes (T1D) risk. Epigenetics and Chromatin, 15(1), 1-21. DOI Scopus1 WoS1 Europe PMC2
2022	Rezaie, N., Bayati, M., Hamidi, M., Tahaei, M. S., Khorasani, S., Lovell, N. H., . . . Alinejad-Rokny, H. (2022). Somatic point mutations are enriched in non-coding RNAs with possible regulatory function in breast cancer. Communications Biology, 5(1), 1-13. DOI Scopus3 WoS3 Europe PMC2
2022	Smith, M. D., Leemaqz, S. Y., Jankovic-Karasoulos, T., McAninch, D., McCullough, D., Breen, J., . . . Pillman, K. A. (2022). Haemolysis Detection in MicroRNA-Seq from Clinical Plasma Samples. Genes, 13(7), 1288-1-1288-15. DOI Scopus4 WoS3 Europe PMC4
2022	McClure, B. J., Pal, M., Heatley, S. L., Rehn, J., Schutz, C., Breen, J., . . . White, D. L. (2022). Two novel cases of NUTM1-rearranged B-cell acute lymphoblastic leukaemia presenting with high-risk features. British Journal of Haematology, 196(6), 1407-1411. DOI Scopus2 WoS2 Europe PMC2
2022	Bournazos, A. M., Riley, L. G., Bommireddipalli, S., Ades, L., Akesson, L. S., Al-Shinnag, M., . . . Williams, M. G. (2022). Standardized practices for RNA diagnostics using clinically accessible specimens reclassifies 75% of putative splicing variants. Genetics in Medicine, 24(1), 130-145. DOI Scopus30 WoS28 Europe PMC23
2022	Bersten, D. C., Sullivan, A. E., McDougal, D., Breen, J., Fitzsimmons, R. L., Muscat, G. E. O., . . . Whitelaw, M. L. (2022). Core and Flanking bHLH-PAS:DNA interactions mediate specificity and drive obesity. DOI
2022	Kimura, S., Montefiori, L., Iacobucci, I., Zhao, Y., Gao, Q., Paietta, E. M., . . . Mullighan, C. G. (2022). Enhancer retargeting of CDX2 and UBTF::ATXN7L3 define a subtype of high-risk B-progenitor acute lymphoblastic leukemia. Blood, 139(24), 3519-3531. DOI Scopus12 WoS12 Europe PMC9
2022	Bogias, J., Pederson, S., Leemaqz, S., Smith, M., McAninch, D., Jankovic-Karasoulos, T., . . . Roberts, C. (2022). Placental transcription profiling in 6-23 weeks’ gestation reveals differential transcript usage in early development. DOI
2022	Smith, M., Leemaqz, S., Jankovic-Karasoulos, T., McCullough, D., McAninch, D., Breen, J., . . . Pillman, K. (2022). DraculR: A web based application for <i>in silico</i> haemolysis detection in high throughput small RNA sequencing data. DOI
2022	Mullany, S., Marshall, H., Zhou, T., Thomson, D., Schmidt, J. M., Qassim, A., . . . Craig, J. E. (2022). RNA Sequencing of Lens Capsular Epithelium Implicates Novel Pathways in Pseudoexfoliation Syndrome. Investigative Ophthalmology and Visual Science, 63(3), 26-1-26-17. DOI Scopus4 WoS4 Europe PMC1
2022	Arthurs, A. L., Smith, M. D., Hintural, M. D., Breen, J., McCullough, D., Thornton, F. I., . . . Roberts, C. T. (2022). Placental Inflammasome mRNA Levels Differ by Mode of Delivery and Fetal Sex. Frontiers in immunology, 13, 1-15. DOI Scopus1 WoS1
2021	Richards, S. M., Li, L., Breen, J., Hovhannisyan, N., Estrada, O., Gasparyan, B., . . . Zhang, H. (2021). Recovery of Chloroplast Genomes from Medieval Millet Grains Excavated from the Areni-1 Cave in Southern Armenia. Scientific Reports. DOI
2021	Tangseefa, P., Martin, S. K., Chin, P. Y., Breen, J., Mah, C. Y., Baldock, P. A., . . . Zannettino, A. C. W. (2021). The mTORC1 complex in pre-osteoblasts regulates whole-body energy metabolism independently of osteocalcin. Bone Research, 9(1), 10-1-10-17. DOI Scopus2 WoS3 Europe PMC3
2021	Heng, S., Samarajeewa, N., Wang, Y., Paule, S. G., Breen, J., & Nie, G. (2021). Podocalyxin promotes an impermeable epithelium and inhibits pro-implantation factors to negatively regulate endometrial receptivity. Scientific Reports, 11(1), 24016-1-24016-14. DOI Scopus2 WoS2 Europe PMC1
2021	Liu, N., Sadlon, T., Wong, Y. Y., Pederson, S. M., Breen, J., & Barry, S. (2021). 3DFAACTS-SNP: Using Regulatory T Cell-specific Epigenomics Data to Uncover Candidate Mechanisms of Type-1 Diabetes (T1D) risk. DOI
2021	Skerrett-Byrne, D. A., Nixon, B., Bromfield, E. G., Breen, J., Trigg, N. A., Stanger, S. J., . . . Schjenken, J. E. (2021). Transcriptomic analysis of the seminal vesicle response to the reproductive toxicant acrylamide. BMC Genomics, 22(1), 728-1-728-22. DOI Scopus5 WoS5 Europe PMC3
2021	Smith, M. D., Pillman, K., Jankovic-Karasoulos, T., McAninch, D., Wan, Q., Bogias, K. J., . . . Roberts, C. T. (2021). Large-scale transcriptome-wide profiling of microRNAs in human placenta and maternal plasma at early to mid gestation. RNA biology, 18(Suppl. 1), 507-520. DOI Scopus15 WoS13 Europe PMC13
2021	Liu, N., Low, W. Y., Alinejad-Rokny, H., Pederson, S., Sadlon, T., Barry, S., & Breen, J. (2021). Seeing the forest through the trees: prioritising potentially functional interactions from Hi-C. Epigenetics & chromatin, 14(1), 1-17. DOI
2021	Zhou, J., Cavagnaro, T. R., De Bei, R., Nelson, T. M., Stephen, J. R., Metcalfe, A., . . . Rodriguez Lopez, C. M. (2021). Wine terroir and the soil bacteria: an amplicon sequencing-based assessment of the Barossa Valley and its sub-regions. Frontiers in Microbiology, 11, 597944-1-597944-15. DOI Scopus6 WoS6 Europe PMC3
2021	Knight, L. S. W., Ruddle, J. B., Taranath, D. A., Goldberg, I., Smith, J. E. H., Gole, G., . . . Craig, J. E. (2021). Childhood and early-onset glaucoma classification and genetic profile in a large Australasian disease registry. Ophthalmology, 128(11), 1549-1560. DOI Scopus18 WoS13 Europe PMC7
2021	Dini, P., Kalbfleisch, T., Uribe-Salazar, J. M., Carossino, M., Ali, H. E. -S., Loux, S. C., . . . Ball, B. A. (2021). Parental bias in expression and interaction of genes in the equine placenta.. Proceedings of the National Academy of Sciences of the United States of America, 118(16), e2006474118. DOI Scopus11 WoS9 Europe PMC3
2021	Mullany, S., Souzeau, E., Klebe, S., Zhou, T., Knight, L. S. W., Qassim, A., . . . Siggs, O. M. (2021). A novel GSN variant outside the G2 calcium-binding domain associated with Amyloidosis of the Finnish type. Human Mutation, 42(7), 818-826. DOI Scopus5 WoS5 Europe PMC4
2021	Fabres, P. J., Anand, L., Sai, N., Pederson, S., Zheng, F., Stewart, A. A., . . . David, R. (2021). Tissue and regional expression patterns of dicistronic tRNA-mRNA transcripts in grapevine (Vitis vinifera) and their evolutionary co-appearance with vasculature in land plants. Horticultural Reviews, 8(1), 137-1-137-15. DOI Scopus2 WoS3 Europe PMC1
2021	Dinh, D. T., Breen, J., Nicol, B., Smith, K. M., Nicholls, M., Emery, A., . . . Russell, D. L. (2021). Progesterone receptor-A isoform interaction with RUNX transcription factors controls chromatin remodelling at promoters during ovulation. DOI
2021	Rezaie, N., Bayati, M., Tahaei, M. S., Hamidi, M., Khorasani, S., Lovell, N., . . . Alinejad-Rokny, H. (2021). Somatic point mutations are enriched in long non-coding RNAs with possible regulatory function in breast cancer. DOI
2021	Downes, C. E. J., McClure, B. J., Bruning, J. B., Page, E., Breen, J., Rehn, J., . . . White, D. L. (2021). Acquired JAK2 mutations confer resistance to JAK inhibitors in cell models of acute lymphoblastic leukemia. NPJ Precision Oncology, 5(1), 1-13. DOI Scopus9 WoS8 Europe PMC6
2021	Mosnier, C., Jarousse, A., Madrange, P., Balouzat, J., Guillier, M., Pirlo, G., . . . Veysset, P. (2021). Evaluation of the contribution of 16 European beef production systems to food security. AGRICULTURAL SYSTEMS, 190, 13 pages. DOI WoS13
2021	Rezaie, N., Bayati, M., Tahaei, M. S., Hamidi, M., Khorasani, S., Lovell, N., . . . Rokny, H. A. (2021). Somatic point mutations are enriched in long non-coding RNAs with possible regulatory function in breast cancer. DOI
2020	Ward, C., Ludington, A., Breen, J., & Baxter, S. (2020). Genomic evolutionary analysis in R with geaR. DOI
2020	Liu, N., Low, W. Y., Alinejad-Rokny, H., Pederson, S., Sadlon, T., Barry, S., & Breen, J. (2020). Seeing the forest through the trees: Identifying functional interactions from Hi-C. biorxiv. DOI
2020	Dashti, H., Dehzangi, A., Bayati, M., Breen, J., Lovell, N., Ebrahimi, D., . . . Alinejad-Rokny, H. (2020). Integrative analysis of mutated genes and mutational processes reveals seven colorectal cancer subtypes. DOI
2020	Fabres, P. J., Anand, L., Sai, N., Pederson, S., Zheng, F., Stewart, A., . . . David, R. (2020). Tissue and regional expression patterns of dicistronic tRNA-mRNA transcripts in grapevine (<i>Vitis vinifera</i>) and their evolutionary co-appearance with vasculature in land plants. DOI
2020	Singhal, G., Morgan, J., Jawahar, M. C., Corrigan, F., Jaehne, E. J., Toben, C., . . . Baune, B. T. (2020). Effects of aging on the motor, cognitive and affective behaviors, neuroimmune responses and hippocampal gene expression. Behavioural Brain Research, 383(6), 112501-1-112501-16. DOI Scopus17 WoS15 Europe PMC10
2020	Kennedy, S. A., Jarboui, M. -A., Srihari, S., Raso, C., Bryan, K., Dernayka, L., . . . Kolch, W. (2020). Extensive rewiring of the EGFR network in colorectal cancer cells expressing transforming levels of KRASG13D.. Nature communications, 11(1), 1-14. DOI Scopus31 WoS26 Europe PMC25
2020	Hng, C. H., Camp, E., Anderson, P., Breen, J., Zannettino, A., & Gronthos, S. (2020). HOPX regulates bone marrow-derived mesenchymal stromal cell fate determination via suppression of adipogenic gene pathways. Scientific Reports, 10(1), 1-14. DOI Scopus12 WoS12 Europe PMC7
2020	McClure, B. J., Heatley, S. L., Rehn, J., Breen, J., Sutton, R., Hughes, T. P., . . . White, D. L. (2020). High-risk B-cell acute lymphoblastic leukaemia presenting with hypereosinophilia and acquiring a novel PAX5 fusion on relapse. British Journal of Haematology, 191(2), 301-304. DOI Scopus1 WoS1
2020	Smith, M., Pillman, K., Jankovic-Karasoulos, T., McAninch, D., Wan, Q., Bogias, J., . . . Roberts, C. (2020). Large-scale transcriptome-wide profiling of microRNAs in human placenta and maternal plasma at early to mid gestation. DOI
2020	Breen, J., McAninch, D., Jankovic-Karasoulos, T., McCullough, D., Smith, M., Bogias, K. J., . . . Roberts, C. (2020). Temporal placental genome wide expression profiles reflect three phases of utero-placental blood flow during early to mid human gestation. DOI
2020	Zhou, J., Cavagnaro, T., De Bei, R., Nelson, T., Stephen, J., Metcalfe, A., . . . Rodríguez López, C. (2020). Wine terroir and the soil microbiome: an amplicon sequencing–based assessment of the Barossa Valley and its sub-regions. DOI
2020	Brown, C. Y., Sadlon, T., Hope, C. M., Wong, Y. Y., Wong, S., Liu, N., . . . Barry, S. C. (2020). Molecular Insights Into Regulatory T-Cell Adaptation to Self, Environment, and Host Tissues: Plasticity or Loss of Function in Autoimmune Disease. Frontiers in Immunology, 11(September), 1-17. DOI Scopus11 WoS9 Europe PMC9
2020	Liu, N., Sadlon, T., Wong, Y. Y., Pederson, S., Breen, J., & Barry, S. C. (2020). 3DFAACTS-SNP: Using regulatory T cell-specific epigenomics data to uncover candidate mechanisms of Type-1 Diabetes (T1D) risk. biorxiv. DOI
2019	Siggs, O. M., Souzeau, E., Breen, J., Qassim, A., Zhou, T., Dubowsky, A., . . . Craig, J. E. (2019). Autosomal dominant nanophthalmos and high hyperopia associated with a C-terminal frameshift variant in MYRF. Molecular Vision, 25, 527-534. Scopus18 WoS16 Europe PMC13
2019	Hatzirodos, N., Hummitzsch, K., Irving-Rodgers, H. F., Breen, J., Perry, V. E. A., Anderson, R. A., & Rodgers, R. J. (2019). Transcript abundance of stromal and thecal cell related genes during bovine ovarian development. PLoS ONE, 14(3), e0213575-1-e0213575-16. DOI Scopus22 WoS22 Europe PMC17
2019	Crowe-Riddell, J. M., Simões, B. F., Partridge, J. C., Hunt, D. M., Delean, S., Schwerdt, J. G., . . . Sanders, K. L. (2019). Phototactic tails: evolution and molecular basis of a novel sensory trait in sea snakes. Molecular Ecology, 28(8), 1-16. DOI Scopus14 WoS12 Europe PMC6
2019	Morgan, J. A., Singhal, G., Corrigan, F., Jaehne, E. J., Jawahar, M. C., Breen, J., . . . Baune, B. T. (2019). Ceasing exercise induces depression-like, anxiety-like, and impaired cognitive-like behaviours and altered hippocampal gene expression. Brain Research Bulletin, 148, 118-130. DOI Scopus16 WoS17 Europe PMC10
2019	Lim, M., Brown, H. M., Kind, K. L., Breen, J., Anastasi, M. R., Ritter, L. J., . . . Dunning, K. R. (2019). Haemoglobin expression in in vivo murine preimplantation embryos suggests a role in oxygen-regulated gene expression. Reproduction, Fertility and Development, 31(4), 724-734. DOI Scopus6 WoS6 Europe PMC4
2019	Weyrich, L. S., Farrer, A. G., Eisenhofer, R., Arriola Martinez, L., Young, J., Selway, C. A., . . . Cooper, A. (2019). Laboratory contamination over time during low-biomass sample analysis. Molecular ecology resources, 19(4), 982-996. DOI Scopus117 WoS114 Europe PMC79
2019	Singhal, G., Morgan, J., Jawahar, M. C., Corrigan, F., Jaehne, E. J., Toben, C., . . . Baune, B. T. (2019). The effects of short-term and long-term environmental enrichment on locomotion, mood-like behavior, cognition and hippocampal gene expression. Behavioural Brain Research, 368, 111917-1-111917-10. DOI Scopus22 WoS18 Europe PMC11
2019	Dinh, D. T., Breen, J., Akison, L. K., DeMayo, F. J., Brown, H. M., Robker, R. L., & Russell, D. L. (2019). Tissue-specific progesterone receptor-chromatin binding and the regulation of progesterone-dependent gene expression. Scientific Reports, 9(1), 11966-1-11966-14. DOI Scopus24 WoS13 Europe PMC16
2019	Singhal, G., Morgan, J., Jawahar, M. C., Corrigan, F., Jaehne, E. J., Toben, C., . . . Baune, B. T. (2019). Short-term environmental enrichment, and not physical exercise, alleviate cognitive decline and anxiety from middle age onwards without affecting hippocampal gene expression. Cognitive, Affective and Behavioral Neuroscience, 19(5), 1143-1169. DOI Scopus15 WoS14 Europe PMC11
2019	Wan, Q., Yiner-Lee Leemaqz, S., Pederson, S. M., McCullough, D., McAninch, D. C., Jankovic-Karasoulos, T., . . . Bianco-Miotto, T. (2019). Quality control measures for placental sample purity in DNA methylation array analyses.. Placenta, 88, 8-11. DOI Scopus2 WoS1 Europe PMC2
2019	Breen, J., & Rabanus-Wallace, M. T. (2019). New tricks for old wheat.. Nature Plants, 5(11), 1108-1109. DOI
2019	Kedzior, S., Bianco-Miotto, T., Breen, J., Diener, K. R., Donnelley, M. W., Dunning, K. R., . . . Rumbold, A. R. (2019). It takes a community to conceive: an analysis of the scope, nature and accuracy of online sources of health information for couples trying to conceive. Reproductive Biomedicine and Society Online, 9, 48-63. DOI Scopus8 Europe PMC7
2019	Ambler, S., Ball, C., Barrett, D., Batchelor, D., Bazeley, K., Bexton, S., . . . Woodroff, C. (2019). Thank you to our reviewers. IN PRACTICE, 41(1), 41.
2018	Weyrich, L., Farrer, A., Eisenhofer, R., Arriola, L., Young, J., Selway, C., . . . Cooper, A. (2018). Laboratory contamination over time during low-biomass sample analysis. DOI
2018	Alaux, M., Rogers, J., Letellier, T., Flores, R., Alfama, F., Pommier, C., . . . Breen, J. (2018). Linking the International Wheat Genome Sequencing Consortium bread wheat reference genome sequence to wheat genetic and phenomic data.. Genome biology, 19(1), 1-10. DOI WoS159 Europe PMC94
2018	Mayne, B., Shalem, L., Buckberry, S., Rodriguez Lopez, C. M., Roberts, C., Bianco-Miotto, T., & Breen, J. (2018). msgbsR: An R package for analysing methylation-sensitive restriction enzyme sequencing data. Scientific Reports, 8(1), 2190-1-2190-8. DOI Scopus9 WoS5 Europe PMC5
2018	MacLennan, A. H., Kruer, M. C., Baynam, G., Moreno-De-Luca, A., Wilson, Y. A., Zhu, C., . . . Gecz, J. (2018). Cerebral palsy and genomics: an international consortium. Developmental Medicine and Child Neurology, 60(2), 209-210. DOI Scopus19 WoS17 Europe PMC11
2018	Sadlon, T., Brown, C. Y., Bandara, V., Hope, C. M., Schjenken, J. E., Pederson, S. M., . . . Barry, S. C. (2018). Unravelling the molecular basis for regulatory T-cell plasticity and loss of function in disease. Clinical and Translational Immunology, 7(2), e1011-1-e1011-15. DOI Scopus21 WoS16 Europe PMC9
2018	Estrada, O., Breen, J., Richards, S. M., & Cooper, A. (2018). Ancient plant DNA in the genomic era. Nature Plants, 4(7), 394-396. DOI Scopus20 WoS16 Europe PMC6
2018	Tikhomirova, A., Trappetti, C., Standish, A., Zhou, Y., Breen, J., Pederson, S., . . . Kidd, S. (2018). Specific growth conditions induce a Streptococcus pneumoniae non-mucoidal, small colony variant and determine the outcome of its co-culture with Haemophilus influenzae. Pathogens and disease, 76(7), 11 pages. DOI Scopus6 WoS7 Europe PMC5
2017	Xie, H., Konate, M., Sai, N., Gebremicael Tesfamicael, K., Cavagnaro, T., Gilliham, M., . . . Rodriguez Lopez, C. M. (2017). Environmental Conditions And Agronomic Practices Induce Consistent Global Changes In DNA Methylation Patterns In Grapevine (Vitis vinifera cv Shiraz). BioRxiv. DOI
2017	Rabanus-Wallace, M., Wooller, M., Zazula, G., Shute, E., Jahren, A., Kosintsev, P., . . . Cooper, A. (2017). Megafaunal isotopes reveal role of increased moisture on rangeland during late Pleistocene extinctions. Nature Ecology & Evolution, 1(5), 0125-1-0125-5. DOI Scopus42 WoS39 Europe PMC8
2017	Hyles, J., Vautrin, S., Pettolino, F., MacMillan, C., Stachurski, Z., Breen, J., . . . Spielmeyer, W. (2017). Repeat-length variation in a wheat cellulose synthase-like gene is associated with altered tiller number and stem cell wall composition. Journal of Experimental Botany, 68(7), 1519-1529. DOI Scopus28 WoS28 Europe PMC21
2017	Mayne, B., Leemaqz, S., Smith, A., Breen, J., Roberts, C., & Bianco-Miotto, T. (2017). Accelerated placental aging in early onset preeclampsia pregnancies identified by DNA methylation.. Epigenomics, 9(3), 279-289. DOI Scopus75 WoS65 Europe PMC46
2017	Weyrich, L., Duchene, S., Soubrier, J., Arriola, L., Llamas, B., Breen, J., . . . Cooper, A. (2017). Neanderthal behaviour, diet, and disease inferred from ancient DNA in dental calculus. Nature, 544(7650), 357-361. DOI Scopus310 WoS270 Europe PMC134
2017	Rabanus-Wallace, M. T., Wooller, M. J., Zazula, G. D., Shute, E., Jahren, A. H., Kosintsev, P., . . . Cooper, A. (2017). Correction: Corrigendum: Megafaunal isotopes reveal role of increased moisture on rangeland during late Pleistocene extinctions (Nature Ecology & Evolution, (2017), 1, 5, (0125), 10.1038/s41559-017-0125). Nature Ecology and Evolution, 1(7), 1 page. DOI
2017	Xie, H., Konate, M., Sai, N., Tesfamicael, K., Cavagnaro, T., Gilliham, M., . . . Lopez, C. (2017). Global DNA methylation patterns can play a role in defining terroir in grapevine (Vitis vinifera cv. Shiraz). Frontiers in Plant Science, 8, 1860-1-1860-16. DOI Scopus38 WoS35 Europe PMC20
2016	Breen, J., Mur, L. A., Sivakumaran, A., Akinyemi, A., Wilkinson, M., & Rodriguez Lopez, C. M. (2016). Botrytis cinerea loss and restoration of virulence during in vitro culture follows flux in global DNA methylation. International Journal of Molecular Sciences, 23(6), 3034-1-3034-49. DOI Scopus6 WoS4 Europe PMC4
2016	Mayne, B., Bianco-Miotto, T., Buckberry, S., Breen, J., Clifton, V., Shoubridge, C., & Roberts, C. (2016). Large scale gene expression meta-analysis reveals tissue-specific, sex-biased gene expression in humans. Frontiers in Genetics, 7(OCT), 183-1-183-14. DOI Scopus62 WoS60 Europe PMC55
2016	Czechowski, P., Clarke, L. J., Breen, J., Cooper, A., & Stevens, M. I. (2016). Antarctic eukaryotic soil diversity of the Prince Charles Mountains revealed by high-throughput sequencing. Soil Biology and Biochemistry, 95, 112-121. DOI Scopus29 WoS23 Europe PMC2
2016	Bianco-Miotto, T., Mayne, B., Buckberry, S., Breen, J., Rodriguez Lopez, C., & Roberts, C. (2016). Recent progress towards understanding the role of DNA methylation in human placental development. Reproduction, 152(1), 23-30. DOI Scopus58 WoS56 Europe PMC40
2016	Mayne, B., Leemaqz, S., Buckberry, S., Breen, J., Bianco-Miotto, T., & Roberts, C. (2016). Sex differences in the human placental methylome. CLINICAL ENDOCRINOLOGY, 84, 48.
2015	Ellison, A., Rodriguez Lopez, C., Moran, P., Swain, M., Megias, M., Hegarty, M., . . . Consuegra, S. (2015). Epigenetic regulation of sex ratios may explain natural variation in self-fertilization rates. Proceedings of the Royal Society of London. Series B, Containing papers of a Biological character. Royal Society (Great Britain), 282(1819), 1-9. DOI Scopus36 WoS31 Europe PMC13
2015	Young, J., Weyrich, L., Breen, J., Macdonald, L., & 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 Scopus36 WoS28 Europe PMC11
2015	Hurni, S., Scheuermann, D., Krattinger, S. G., Kessel, B., Wicker, T., Herren, G., . . . 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 of USA, 112(28), 8780-8785. DOI Scopus200 WoS193 Europe PMC124
2015	Ellison, A., Rodriguez Lopez, C., Moran, P., Breen, J., Swain, M., Megias, M., . . . Consuegra, S. (2015). Epigenetic regulation of sex-ratios may explain natural variation in self-fertilization rates. Proceedings of the Royal Society of London. Series B, 282(1819), 1-9. DOI
2014	Mago, R., Tabe, L., Vautrin, S., Simkova, H., Kubalakova, M., Upadhyaya, N., . . . Spielmeyer, W. (2014). Major haplotype divergence including multiple germin-like protein genes, at the wheat Sr2 adult plant stem rust resistance locus. BMC Plant Biology, 14(1), 379-1-379-11. DOI Scopus30 WoS26 Europe PMC18
2013	Breen, J., Wicker, T., Shatalina, M., Frenkel, Z., Bertin, I., Philippe, R., . . . Kelle, B. (2013). A physical map of the short arm of wheat chromosome 1A. PLoS One, 8(11), e80272-1-e80272-16. DOI Scopus28 WoS26 Europe PMC17
2011	Mago, R., Simkova, H., Brown-Guedira, G., Dreisigacker, S., Breen, J., Jin, Y., . . . Spielmeyer, W. (2011). Erratum to: An accurate DNA marker assay for stem rust resistance gene Sr2 in wheat (Theor Appl Genet, 10.1007/s00122-010-1482-7). Theoretical and Applied Genetics, 122(4), 745. DOI Scopus1
2011	Mago, R., Brown-Guedira, G., Dreisigacker, S., Breen, J., Jin, Y., Singh, R., . . . Spielmeyer, W. (2011). An accurate DNA marker assay for stem rust resistance gene Sr2 in wheat. Theoretical and Applied Genetics, 122(4), 735-744. DOI Scopus141 WoS134 Europe PMC58
2011	Mago, R., Tabe, L., McIntosh, R., Pretorius, Z., Kota, R., Paux, E., . . . 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 Genetics, 123(4), 615-623. DOI Scopus86 WoS80 Europe PMC41
2011	Zhang, J., Jia, J., Breen, J., & Kong, X. (2011). Recent insertion of a 52-kb mitochondrial DNA segment in the wheat lineage. Functional and Integrative Genomics, 11(4), 599-609. DOI Scopus2 WoS2 Europe PMC2
2011	Parlange, F., Oberhaensli, S., Breen, J., Platzer, M., Taudien, S., Šimková, H., . . . 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 Scopus33 WoS28 Europe PMC26
2010	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), 463-476. DOI Scopus65 WoS59 Europe PMC35
2010	Breen, J., Li, D., Dunn, D. S., Békés, F., Kong, X., Zhang, J., . . . 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(1), 11 pages. DOI Scopus16 WoS14 Europe PMC8
2010	Breen, J., Wicker, T., Kong, X., Zhang, J., Ma, W., Paux, E., . . . 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(1), 15 pages. DOI Scopus12 WoS10 Europe PMC8
2010	Choulet, F., Wicker, T., Rustenholz, C., Paux, E., Salse, J., Leroy, P., . . . Feuillet, C. (2010). Megabase level sequencing reveals contrasted organization and evolution patterns of the wheat gene and transposable element spaces. Plant Cell, 22(6), 1686-1701. DOI Scopus225 WoS207 Europe PMC172
2007	Moolhuijzen, P., Dunn, D. S., Bellgard, M., Carter, M., Jia, J., Kong, X., . . . Appels, R. (2007). Wheat genome structure and function: Genome sequence data and the International Wheat Genome Sequencing Consortium. Australian Journal of Agricultural Research, 58(6), 470-475. DOI Scopus13 WoS9
2004	Herlihy, M., McCarthy, J., Breen, J., & Moles, R. (2004). Effects over time of fertiliser P and soil series on P balance, soil-test P and herbage production. IRISH JOURNAL OF AGRICULTURAL AND FOOD RESEARCH, 43(2), 147-160. WoS21
2002	Breen, J. (2002). Transitions in the concept of chronic pain. ADVANCES IN NURSING SCIENCE, 24(4), 48-59. DOI WoS24 Europe PMC17
1999	Breen, J. (1999). Aromatherapy for pregnancy and childbirth.. JOURNAL OF NURSE-MIDWIFERY, 44(3), 336.

Book Chapters

Year	Citation
2022	Estrada, O., Richards, S. M., & Breen, J. (2022). Discovering the Secrets of Ancient Plants: Recovery of DNA from Museum and Archaeological Plant Specimens. In Methods in Molecular Biology (Vol. 2512, pp. 261-267). Springer US. DOI

Conference Papers

Year	Citation
2022	Mullany, S., Zhou, T., Qassim, A., Marshall, H., Knight, L. S. W., Hollitt, G., . . . Craig, J. E. (2022). Transcriptomic analysis of the human lens capsular epithelium in pseudoexfoliation disease. In CLINICAL AND EXPERIMENTAL OPHTHALMOLOGY Vol. 49 (pp. 910). WILEY.
2022	Knight, L. S. W., Ruddle, J. B., Taranath, D. A., Goldberg, I., Smith, J. E., Gole, G., . . . Craig, J. E. (2022). Childhood and early-onset glaucoma classification and genetic profile in the Australian and New Zealand Registry of Advanced Glaucoma: An update. In CLINICAL AND EXPERIMENTAL OPHTHALMOLOGY Vol. 49 (pp. 854-855). WILEY.
2022	Mullany, S., Souzeau, E., Klebe, S., Zhou, T., Knight, L. S. W., Qassim, A., . . . Siggs, O. M. (2022). The novel gelsolin GSN:c.1477T>C variant is associated with the systemic and ophthalmic phenotype of amyloidosis of the Finnish type. In CLINICAL AND EXPERIMENTAL OPHTHALMOLOGY Vol. 49 (pp. 893). WILEY.
2021	Ciobanu, L., Heathcote, A., Breen, J., Rogasch, N., Stankov, L., Clark, S., & Aidman, E. (2021). From Genes to Personalised Cognitive Training: Mapping the Genetic Architectures of Cognitive Functioning. In APPLYING NEUROSCIENCE TO PERFORMANCE: FROM REHABILITATION TO HUMAN COGNITIVE AUGMENTATION. Rome, Italy.
2019	Panir, K., Schjenken, J. E., Breen, J., Greaves, E., Robertson, S. A., & Hull, M. L. (2019). Lesion Development in Endometriosis is Regulated by <i>miR</i>-<i>223</i> Mediated Macrophage Activity.. In REPRODUCTIVE SCIENCES Vol. 26 (pp. 375A-376A). Paris, FRANCE: SAGE PUBLICATIONS INC.
2018	Roberts, C. T., Mayne, B., Leemaqz, S., McAninch, D., Breen, J., Andraweera, P., & Bianco-Miotto, T. (2018). PLACENTAL NON-CODING RNA EXPRESSION CHANGES DYNAMICALLY ACROSS GESTATION. In PLACENTA Vol. 69 (pp. E2). Tokyo, JAPAN: W B SAUNDERS CO LTD.
2003	Rudolph, J. G., Durocher, J., Breen, J., Walters, B., Qiu, P., Shandilya, H., . . . Gerard, G. F. (2003). Detection of gene variants utilizing Surveyor<SUP>TM</SUP> CEL nuclease detection technology and various DNA separation platforms.. In AMERICAN JOURNAL OF HUMAN GENETICS Vol. 73 (pp. 442). LOS ANGELES, CALIFORNIA: UNIV CHICAGO PRESS.
2002	Terry, P. F., Frueh, F., Taylor, N., Breen, J., & Marino, M. A. (2002). Determining the genetic basis of pseudoxanthoma elasticum (PXE): A consortium driven research network partnering an international non-profit patient advocacy organization, academic institutions, and a biotechnology corporation.. In AMERICAN JOURNAL OF HUMAN GENETICS Vol. 71 (pp. 172). BALTIMORE, MARYLAND: UNIV CHICAGO PRESS.

Conference Items

Year	Citation
2022	Thomson, A., Rehn, J., Heatley, S., Eadie, L., McClure, B., Page, E., . . . White, D. (2022). Benchmarking the detection rate of IGH gene fusions in B-cell Acute Lymphoblastic Leukaemia. Poster session presented at the meeting of Australian Bioinformatics and Computational Biology Society (ABACBS) Conference.
2021	Mullany, S., Souzeau, E., Klebe, S., Zhou, T., Knight, L., Qassim, A., . . . Siggs, O. M. (2021). A novel gelsolin variant associated with Familial Amyloidosis of the Finnish type in an Australian family. Poster session presented at the meeting of Abstracts of the Association for Research in Vision & Ophthalmology 2021 Annual Meeting (ARVO), as published in Investigative Ophthalmology & Visual Science. virtual online: Association for Research in Vision & Ophthalmology.
2021	Eadie, L., Heatley, S., McClure, B., Rehn, J., Schutz, C., Breen, J., . . . White, D. (2021). Next Generation Genomic Analyses Inform Druggable Targets In T-All Patients. Poster session presented at the meeting of 4th International T-ALL/T-NHL conference: T-ALL2020: Omics, genetics and therapy.
2021	Eadie, L., Heatley, S., McClure, B., Rehn, J., Schutz, C., Breen, J., . . . White, D. (2021). Next Generation Genomic Analyses Inform Druggable Targets In T-All Patients. Poster session presented at the meeting of 12th Biennial Childhood Leukemia and Lymphoma Symposium (CLLS).
2021	Heatley, S., Rehn, J., Breen, J., Moore, A., Sutton, R., Osborn, M., & White, D. (2021). Using single cell mRNAseq to interrogate the genomic consequences of Ph-like acute lymphoblastic leukaemia in adolescents. Poster session presented at the meeting of 12th Biennial Childhood Leukemia and Lymphoma Symposium (CLLS).
2021	Ciobanu, L., Stankov, L., Heathcote, A., Clark, S., Breen, J., Rogasch, N., . . . Aidman, E. (2021). Mapping the genetic architectures of cognitive functioning. Poster session presented at the meeting of GeneMappers 2021. Virtual.
2020	Eadie, L., Heatley, S., McClure, B., Schutz, C., Breen, J., Hughes, T., . . . White, D. (2020). Next Generation Genomic Analyses Inform Druggable Targets In T-All Patients. Poster session presented at the meeting of Australian & New Zealand Children’s Haematology/Oncology Group.
2020	Downes, C. E. J., McClure, B. J., Rehn, J., Breen, J., Bruning, J. B., Yeung, D. T., & White, D. L. (2020). Acquired Mutations within the JAK2 Kinase Domain Confer Resistance to JAK Inhibitors in an <i>in Vitro</i> model of a High-Risk Acute Lymphoblastic Leukemia. Poster session presented at the meeting of BLOOD. ELECTR NETWORK: AMER SOC HEMATOLOGY. DOI WoS1
2020	Eadie, L. N., Rehn, J., Heatley, S. L., McClure, B. J., Schutz, C. S., Breen, J., . . . White, D. L. (2020). Next Generation Genomic Analyses in T-ALL Patients Identify Recurrent and Novel Genomic Abnormalities. Poster session presented at the meeting of BLOOD. ELECTR NETWORK: AMER SOC HEMATOLOGY. DOI WoS1
2020	Rehn, J. A., Breen, J., Heatley, S. L., McClure, B. J., Eadie, L. N., Schutz, C. E., . . . White, D. L. (2020). Targeted pseudo-alignment technique for rapid and accurate identification of disease-causing variants in acute lymphoblastic leukaemia. Poster session presented at the meeting of 14th Annual Florey Postgraduate Conference. Adelaide, South Australia.
2020	Rehn, J. A., Breen, J., Heatley, S. L., McClure, B. J., Eadie, L. N., Schutz, C. E., . . . White, D. L. (2020). Pseudo-alignment technique for accurate detection of disease-causing variants in acute lymphoblastic leukaemia. Poster session presented at the meeting of Australian Bioinformatics and Computational Biology Society (ABACBS) 2020 National Conference. Canberra, ACT.
2020	Breen, J., Smith, M., McAninch, D., Jankovic-Karasoulos, T., McCullough, D., Pederson, S. M., . . . Roberts, C. (2020). Defining Co-expression Patterns and Molecular Pathways of the Placenta During Early Pregnancy.. Poster session presented at the meeting of REPRODUCTIVE SCIENCES. Vancouver, CANADA: SPRINGER HEIDELBERG.
2020	Wan, Q., Breen, J., Leemaqz, S. Y. -L., Pederson, S. M., Jankovic-Karasoulos, T., McAninch, D. C., . . . Bianco-Miotto, T. (2020). Characterisation of Placental DNA Methylation Across Early Human Gestation.. Poster session presented at the meeting of REPRODUCTIVE SCIENCES. Vancouver, CANADA: SPRINGER HEIDELBERG.
2019	Yeung, D., Greenwood, M., Rehn, J., Heatley, S., McClure, B., Eadie, L., . . . White, D. (2019). High risk genomic alterations identified at the time of diagnosis are strongly associated with MRD and subsequent poor outcomes in AYA ALL patients treated on a pediatric inspired chemotherapy regimen. Poster session presented at the meeting of Blood. Orlando, CA: American Society of Hematology. DOI
2019	Eadie, L., Heatley, S. L., McClure, B. J., Rehn, J. A., Breen, J., Hughes, T. P., . . . White, D. L. (2019). Exploration of the Genomic Diversity in T-ALL Patients Using mRNA Sequencing. Poster session presented at the meeting of 1st European Society of Haematology (ESH) Translational Conference on ALL. Berlin, Germany.
2019	Eadie, L., Heatley, S. L., McClure, B. J., Rehn, J. A., Breen, J., Hughes, T. P., . . . White, D. L. (2019). Exploration of the Genomic Diversity in T-ALL Patients Using mRNA Sequencing. Poster session presented at the meeting of ASMR Annual Scientific Meeting. Adelaide, South Australia.
2019	Rehn, J. A., Breen, J., Heatley, S. L., McClure, B. J., Eadie, L., Schutz, C. E., . . . White, D. L. (2019). Investigating “alignment-free” computational techniques for the accurate identification of Acute Lymphoblastic Leukaemia (ALL) gene fusion events. Poster session presented at the meeting of SAHMRI Annual Scientific Meeting. Adelaide, South Australia.
2019	Heatley, S. L., McClure, B. J., Eadie, L. N., Rehn, J. A., Breen, J., Hughes, T. P., . . . White, D. L. (2019). Exploring the genomic diversity of AYA and adult high-risk B-ALL cases by mRNA sequencing. Poster session presented at the meeting of SAHMRI Annual Scientific Meeting. Adelaide, South Australia.
2015	Miller, C., Franks, C., Breen, J., Weyrich, L., Soubrier, J., Llamas, B., . . . Cooper, A. (2015). Open access to ancient human DNA: An Australian Centre for Ancient DNA (ACAD) and University Libraries collaboration. Poster session presented at the meeting of Proceedings of eResearch Australasia 2016. Brisbane, Australia: eResearch Australasia.

Theses

Year Citation
2009 Breen, J. (2009). Assembly of a Complex Genome: Defining Elements of Structure and Function. (PhD Thesis).
Internet Publications

Year Citation
2015 Farrer, A. G., & Breen, J. (2015). OAGR: a brand new genome database. Australian Centre for Ancient DNA - Blog.
Datasets

Year Citation
2017 Breen, J., & Rodriguez Lopez, C. M. (2017). Virulent/avirulent Botrytis cinerea whole genome/methylome sequence.

Year	Citation
2009	Breen, J. (2009). Assembly of a Complex Genome: Defining Elements of Structure and Function. (PhD Thesis).

Year	Citation
2015	Farrer, A. G., & Breen, J. (2015). OAGR: a brand new genome database. Australian Centre for Ancient DNA - Blog.

Year	Citation
2017	Breen, J., & Rodriguez Lopez, C. M. (2017). Virulent/avirulent Botrytis cinerea whole genome/methylome sequence.

Software

Year	Citation
2017	Sai, N., Rodriguez Lopez, C. M., Bogias, K., Pederson, S., Burgess, A., Breen, J., . . . David, R. (2017). Bioinformatic pipeline to detect di-cistronic RNA transcripts from RNA-sequencing data [Computer Software].
2016	Mayne, B., Leemaqz, S., Buckberry, S., rodriguez lopez, C. M., roberts, C., bianco-miotto, T., & Breen, J. (2016). msgbsR: an R package for analysing methylation sensitive genotyping by sequencing data [Computer Software]. github.

Filesets

Year	Citation
-	Weyrich, L., Farrer, A., Philipona, R. E., Handsley-Davis, M., Martinez, L. A., Young, J., . . . Breen, J. (n.d.). Laboratory contamination over time during low-biomass sample analysis. DOI
-	Crowe-Riddell, J., Simoes, B., Schwerdt, J., Ludington, A., Breen, J., & Sanders, K. (n.d.). Phototactic tails manuscript ESM-Files. DOI

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
2022	Co-Supervisor	Indigenous Genomics, Epigenetics & Applications to Disease	Doctor of Philosophy	Doctorate	Full Time	Samuel Arthur Luke Godwin
2022	Co-Supervisor	Standardising clinical sequencing analysis workflows for Acute Lymphoblastic Leukaemia (ALL) samples	Master of Philosophy (Medical Science)	Master	Full Time	Miss Ashlee Jean Thomson
2019	Principal Supervisor	Bioinformatic approaches to variant detection and subtype classification in acute lymphoblastic leukaemia	Doctor of Philosophy	Doctorate	Full Time	Miss Jacqueline Ann Rehn

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
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

Committee Memberships

Date	Role	Committee	Institution	Country
2019 - ongoing	Member	NHMRC Investigator Grants Peer Review Working Committee	National Health & Medical Research Council	Australia
2018 - ongoing	Member	National Executive Committee	Australian Bioinformatics & Computational Biology Society (ABACBS)	Australia
2017 - 2019	Chair	Organising Committee	Epigenetics Consortium of South Australia (EpiCSA) Inc	Australia
2017 - 2017	Member	COMBINE Conference Committee	Australian Bioinformatics and Computational Biologu Society	Australia
2016 - 2016	Member	BioinfoSummer 2016 Organising Committee	University of Adelaide	Australia

Memberships

Date Role Membership Country
2015 - ongoing Member Australian Bioinformatics and Computational Biology Society (ABACBS) Australia

Date	Role	Membership	Country
2015 - ongoing	Member	Australian Bioinformatics and Computational Biology Society (ABACBS)	Australia

Email: jimmy.breen@adelaide.edu.au

Jimmy Breen

Available Research Projects

Appointments

Education

Research Interests

Journals

Book Chapters

Conference Papers

Conference Items

Theses

Internet Publications

Datasets

Software

Filesets

Current Higher Degree by Research Supervision (University of Adelaide)

Past Higher Degree by Research Supervision (University of Adelaide)

Committee Memberships

Memberships

Connect With Me

External Profiles

Other Links