
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
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.
-
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
-
Journals
-
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.
-
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.
WoS12020 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.
WoS12020 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.
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. -
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.
- Crowe-Riddell, J., Simoes, B., Schwerdt, J., Ludington, A., Breen, J., & Sanders, K. (n.d.). Phototactic tails manuscript ESM-Files.
-
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
Connect With Me
External Profiles