Bioinfo:RAdelaide

James Breen

Genomics and Bioinformatics Researcher

Email: jimmymbreen at gmail dot com
twitter: wessidepraxis
github: jimmybgammyknee
Google Scholar: Jimmy Breen


Table of Contents

Academic and Professional Positions

Current

2022-
Chief Data Scientist, Black Ochre Data Labs (Indigenous Genomics),
Telethon Kids Institute (Adelaide, SA, Australia)

Associate Professor (Indigenous Genomics),
Australian National University (Canberra, ACT, Australia)

Former

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

Publications

Journal Articles

2024

Panir K, Schjenken JE, Breen J, Chan HY, Greaves E, Robertson S & Hull ML. (2024). RNA sequencing reveals novel molecular mechanisms of endometriosis lesion development in a mouse model. Disease Models & Mechanisms. Accepted 01/10/2024.

Oliva A, Kaphle A, Reguant R, Sng LMF, Twine NA, Malakar Y, Wickramarachchi A, Keller M, Ranbaduge T, Chan EKF, Breen J, Buckberry S, Guennewig B, Haas M, Brown A, Cowley MJ, Thorne N, Jain Y & Bauer D. (2024). Future-proofing genomic data and consent management: a comprehensive review of technology innovations. GigaScience. Accepted 10/04/2024.

Gancheva MR, Kremer K, Breen J, Arthur A, Hamilton-Bruce A, Thomas P, Gronthos S & Koblara S. (2024). Effect of Octamer-binding transcription factor 4 overexpression on the neural induction of human dental pulp stem cells. Stem Cell Reviews and Reports. Accepted 10/01/2024.

2023

Ludington AJ, Hammond JM, Breen J, Deveson IW & Sanders KL. (2023). New chromosome-scale genomes provide insights into marine adaptations of sea snakes (Hydrophis: Elapidae). BMC Biology. Accepted 25/11/2023. doi:10.1186/s12915-023-01772-2.

Chan HY, Tran HM, Breen J, Schjenken JE. & Robertson SA. (2023). The endometrial transcriptome transition preceding receptivity to embryo implantation in mice. BMC Genomics. 24:590. doi:10.1186/s12864-023-09698-3.

Thomson AJ, Rehn JA, Heatley SL, Eadie LN, Page EC, Schutz C, McClure BJ, Sutton R, Dalla-Pozza L, Moore AS, Greenwood M, Kotecha RS, Fong C, Yong ASM, Yeung DT, Breen J & White DL. (2023). Reproducible bioinformatics analysis workflows for detecting IGH gene fusions in B-cell acute lymphoblastic leukaemia patients. Cancers. 15(19): 4731. doi:10.3390/cancers15194731. Co-senior/co-corresponding author

Khurana I, Howard NJ, Maxwell S, Du Preez A, Kaipananickal H, Breen J, Buckberry S, Okabe J, Al-Hasani K, Nakasatien S, Himathongkam T, Cooper ME, Maple-Brown L, Thewjitcharoen Y, Brown A & El-Osta A. (2023). Circulating epigenomic biomarkers correspond with diabetic kidney disease susceptibility in high-risk populations with type 2 diabetes. Diabetes Research and Clinical Practice. Accepted 21/09/2023. doi:10.1016/j.diabres.2023.110918

Buckberry S, Liu X, Poppe D, Tan JP, Sun G, Chen J, Nguyen TV, de Mendoza A, Pflueger J, Frazer T, Vargas-Landín DB, Paynter JM, Smits N, Liu N, Ouyang JF, Rossello FJ, Chy HS, Rackham OJL, Laslett AL, Breen J, Faulkner GJ, Nefzger CM, Polo JM & Lister R. (2023). Transient naive reprogramming corrects hiPS cells functionally and epigenetically. Nature 1–10. doi:10.1038/s41586-023-06424-7.

Dinh DT, Breen J, Nicol B, Bersten D, Emery A, Smith KM, Nicholls M, Wong YY, Barry SC, Yao HH-C, Robker RL & Russell DL. (2023). Progesterone receptor mediates ovulatory transcription through RUNX transcription factor interactions and chromatin remodelling. Nucleic Acids Research. gkad271. doi:10.1093/nar/gkad271.
Preprint: bioRxiv. doi:10.1101/2021.06.17.448908.

Wong YY, Harbison JE, Hope CM, Gundsambuu B, Brown KA, Wong SW, Brown C, Couper JJ, Breen J, Liu N, Pederson SM, Köhne M, Klee K, Schultze J, Beyer M, Sadlon T & Barry SC. (2023). Parallel recovery of chromatin accessibility and gene expression dynamics from frozen human Regulatory T cells. Scientific Reports. 13(1):5506. doi:10.1038/s41598-023-32256-6.

Aldersey JE, Liu N, Tearle R, Breen J, Williams JL & Bottema CDK. (2023). Topologically associating domains in the POLLED region are the same for haplotype-resolved Hi-C reads from Angus x Brahman F1 hybrid fetal tissue. Animal Genetics. Accepted 24/02/2023. doi:10.1111/age.13322.

Smith MD, Leemaqz SY, Jankovic-Karasoulos T, McCullough D, McAninch D, Arthurs AL, Breen J, Roberts CT & Pillman KA. (2023). DraculR: A web-based application for in silico haemolysis detection in high throughput microRNA sequencing data. Genes. 14(2): 448. doi:10.3390/genes14020448.

Eadie LN, Rehn JA, Breen J, Osborn MP, Jessop S, Downes CEJ, Heatley SL, McClure BJ, Yeung DT, Revesz T, Saxon B & White DL. (2023). Case Report: Rare IKZF1 gene fusions identified in neonate with congenital KMT2A-rearranged Acute Lymphoblastic Leukemia. Genes. 14(2): 264, doi:10.3390/genes14020264.

2022

Lim CK, Romeo O, Chilver AP, Tran BM, Flanagan DJ, Kirby EN, Breen J, Vincan E, Warner N, McCartney EM, Van Der Hoek MB, Ruszkiewicz A, Tse E, Beard MR. (2022). Human Liver Organoids as a Patient-derived Model for HBV Infection and Cellular Response. bioRxiv 2022.10.20.513112 doi:10.1101/2022.10.20.513112. PREPRINT

Rehn J, Mayoh C, Heatley SL, McClure BJ, Eadie L, Schutz C, Yeung DT, Cowley M, Breen J & White DL. (2022). RaScALL: Rapid (Ra) screening (Sc) of RNA-seq data for prognostically significant genomic alterations in acute lymphoblastic leukaemia (ALL). PLOS Genetics. Accepted 23/09/2022. Corresponding/Co-Senior Author

Richards SM, Li L, Breen J, Hovhannisyan N, Estrada O, Gasparyan B, Gilliham M, Smith A, Cooper A & Zhang H. (2021). Recovery of Chloroplast Genomes from Medieval Millet Grains Excavated from the Areni-1 Cave in Southern Armenia. Scientific Reports. Accepted 04/08/2022
Preprint: Research Square. doi:10.21203/rs.3.rs-959635/v1.

Smith MD, Leemaqz SY, Jankovic-Karasoulos T, McAninch D, McCullough D, Breen J, Roberts CT, Pillman KA. (2022). Haemolysis Detection in MicroRNA-seq from Clinical Plasma Samples. Genes. 13(7):1288. doi:10.3390/genes13071288

Souzeau E, Siggs O, Mullany S, Schmidt J, Hassall M, Dubowsky A, Chappell A, Breen J, Bae H, Nicholl J, Hadler J, Kearns L, Staffieri S, Hewitt A, Mackey D, Gupta A, Burdon K, Klebe S, Craig J & Mills R. (2021). Diagnostic yield of candidate genes in an Australian corneal dystrophy cohort. Molecular Genetics & Genomic Medicine. Accepted 19/7/2021

Liu N, Sadlon T, Wong YY, Pederson SM, Breen J & Barry SC. (2022). 3DFAACTS-SNP: Using regulatory T cell-specific epigenomics data to uncover candidate mechanisms of Type-1 Diabetes (T1D) risk. Epigenetics & Chromatin. 15,24. doi10.1186/s13072-022-00456-5. Corresponding/Co-Senior Author Preprint version: bioRxiv. doi:10.1101/2020.09.04.279554.

Makinen VP, Rehn J, Breen J, Yeung D & White D. (2022). Multi-cohort transcriptomic subtyping of B-cell acute lymphoblastic leukemia. International Journal of Molecular Sciences. 23(9), 4574. doi:10.3390/ijms23094574.
Preprint version: medRxiv. doi:10.1101/2022.02.17.22270919v1.

Smith MD, Leemaqz SY, Jankovic-Karasoulos T, McCullough D, McAninch D, Breen J, Roberts CT, Pillman KA. (2022). DraculR: A web based application for in silico haemolysis detection in high throughput small RNA sequencing data. Preprint version: medRxiv. doi:10.1101/2022.03.27.22273019. PREPRINT

Dashti H, Dehzangi A, Bayati M, Breen J, Lovell N, Ebrahimi D, Rabiee HR, Alinejad-Rokny H. (2022). Integrative analysis of mutated genes and mutational processes reveals novel mutational biomarkers in colorectal cancer. BMC Bioinformatics. 23, 138. doi:10.1186/s12859-022-04652-8.

Rezaei N, Bayati M, Tahaei MS, Khorasani S, Hamidi N, Lovell N, Breen J, Rabiee H & Alinejad Rokny H. (2022). Somatic point mutations are enriched in long non-coding RNAs with possible regulatory function in breast cancer. Communications Biology. 5, 556. doi:10.1038/s42003-022-03528-0.

Bogias KJ, Pederson SM, Leemaqz S, Smith MD, McAninch D, Jankovic-Karasoulos T, McCullough D, Wan Q, Bianco-Miotto T, Breen J & Roberts CT. (2022). Placental transcription profiling in 6-23 weeks’ gestation reveals differential transcript usage in early development. International Journal of Molecular Sciences. 23(9), 4506. doi:10.3390/ijms23094506.
Preprint version: medRxiv doi:10.1101/2022.03.03.22271882.

Breen J, Mur LAJ, Sivakumaran A, Akinyemi A, Wilkinson MJ & Rodriguez Lopez CM. (2022). 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; doi:10.3390/ijms23063034.
Preprint version: bioRxiv http://biorxiv.org/content/early/2016/08/26/059477.

Mullany S, Marshall H, Zhou T, Thomson D, Schmidt JM, Qassim A, Knight LSW, Hollitt G, Berry EC, Nguyen T, To M-S, Dimasi D, Kuot A, Dubowsky J, Fogarty R, Sun M, Chehade L, Kuruvilla S, Supramaniam D, Hussey M, Breen J, Sharma S, Landers J, Lake S, Mills RA, Hassall MM, Chan WO, Klebe S, Souzeau E, Siggs OM & Craig JE. (2022). RNA sequencing of lens capsular epithelium implicates novel pathways in pseudoexfoliation syndrome. Investigative Ophthalmology & Visual Science. 63(3): 26. doi:10.1167/iovs.63.3.26.

Kimura S, Montefiori L, Iacobucci I, Zhao Y, Gao Q, Paietta EM, Haferlach C, Laird AD, Mead PE, Gu Z, Stock W, Litzow MR, Rowe JM, Luger SM, Hunger SP, Ryland G, Schmidt BM, Ekert PG, Oshlack A, Grimmond S, Rehn J, Breen J, Yeung DT, White DL, Aldoss I, Jabbour EJ, Pui C-H, Meggendorfer M, Walter W, Kern W, Haferlach T, Brady SW, Zhang J, Roberts KG, Blombery P & Mullighan CG. (2022). Enhancer retargeting of CDX2 and UBTF::ATXN7L3 define a subtype of high-risk B-progenitor acute lymphoblastic leukemia. Blood. blood.2022015444. doi:10.1182/blood.2022015444.

Okada T, McIlfatrick S, Hin N, Aryamanesh N, Breen J & St. John JC. (2022). Mitochondrial supplementation of Sus scrofa metaphase II oocytes alters DNA methylation and gene expression profiles of blastocysts. Epigenetics & Chromatin. 15, 12. doi:10.1186/s13072-022-00442-x.

Arthurs AL, Smith MD, Hintural MD, Breen J, McCullough D, Thornton F, Leemaqz S, Dekker GA, Jankovic-Karasoulos T & Roberts CT. (2022). Parturition: the end of tolerance in pregnancy. Frontiers in Immunology. 13: Online 25 Mar 2022 doi:10.3389/fimmu.2022.807750

2021

McClure BJ, Pal M, Heatley SL, Rehn J, Schutz C, Breen J, Venn NC, Sutton R, Khaw SL, Yeung DT & White DL. (2021). Two novel cases of NUTM1-rearranged B-cell acute lymphoblastic leukemia presenting with high-risk features. British Journal of Haematology. 196(6): 1407-1411 doi:10.1111/bjh.17995.

Paule SG, Heng S, Samarajeewa N, Li Y, Wang Y, Webb AI, Young SL, Lessey BA, Hull ML, Breen J, Van de Velde H, Scelwyn M, Vollenhoven B, Rombauts LK & Nie G. (2021). Podocalyxin governs the barrier function of human endometrial epithelium and critically regulates receptivity for embryo implantation. Scientific Reports. 11, 24016. doi:10.1038/s41598-021-03425-2.

Skerrett-Byrne DA, Nixon B, Bromfield EG, Breen J, Trigg NA, Stanger SJ, Bernstein IR, Anderson AL, Lord T, Aitken RJ, Roman SD, Robertson SA & Schjenken JE. (2021). Transcriptomic analysis of the seminal vesicle response to the reproductive toxicant acrylamide. BMC Genomics 22:728. doi:10.1186/s12864-021-07951-1.

Smith MD, Pillman K, Jankovic-Karasoulos T, McAninch D, Wan Q, Bogias KJ, McCullough D, Bianco-Miotto T, Breen J & Roberts CT. (2020). Large-scale transcriptome-wide profiling of microRNAs in human placenta and maternal plasma at early to mid gestation. RNA Biology. 1-14. doi:10.1080/15476286.2021.1963105.

Liu N, Low WY, Alinejad-Rokny H, Pederson SM, Sadlon T, Barry SC & Breen J. (2021). Seeing the forest through the trees: Prioritising potentially functional interactions from Hi-C. Epigenetics & Chromatin. 14(1): 1-17. doi:10.1186/s13072-021-00417-4.

Downes CEJ, McClure BJ, Bruning JB, Page E, Breen J, Rehn J, Yeung DT & White DL. (2021). Acquired mutations within the JAK2 kinase domain confer resistance to type-I and type-II JAK inhibitors in in vitro models of a high-risk acute lymphoblastic leukemia. NPJ Precision Oncology. 5(1): 1-13. doi:10.1038/s41698-021-00215-x.

Mullany S, Souzeau E, Klebe S, Zhou T, Knight LSW, Qassim A, Berry E, Marshall H, Hussey M, Dubowsky A, Hassall MM, Breen J, Hassall M, Mills RA, Craig JE & Siggs OM. (2021). A novel GSN variant affecting gelsolin domain 4 is associated with Familial Amyloidosis of the Finnish type. Human Mutation. 42(7): 818-826. doi:10.1002/humu.24214

Rodriguez Lopez CM, Fabres PJ, Pederson SM, Zheng F, Breen J, Gilliham M, Tricker P, David R, Sai N, Anand L, Stewart A, Clements B & Lampugnani E. (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. Horticulture Research . Accepted 14/04/2021 Preprint: bioRxiv. 10.1101/2020.04.13.039131.

Knight LSW, Ruddle JB, Taranath DA, Goldberg I, Smith JEH, Gole G, Chiang MY, Willett F, D’Mellow G, Breen J, Qassim A, Mullany S, Elder JE, Vincent AL, Staffieri SE, Kearns LS, Mackey DA, Luu S, Siggs OM, Souzeau E & Craig JE. (2021). Childhood and Early-Onset Glaucoma Classification and Genetic Profile in a Large Australasian Disease Registry. Ophthalmology. Online Ahead of print Apr 20; S0161-6420(21)00288-8. doi:10.1016/j.ophtha.2021.04.016

Dini P, Kalbfleisch T, Carossino M, El-Sheikh Ali H, Loux SC, Esteller-Vico A, Norris JK, Anand L, Uribe-Salazar JM, Scoggin KM, Rodriguez Lopez CM, Breen J, Bailey E, Daels P & Ball BA. (2021). Parental bias in placental gene expression: A closer look at reciprocal paternal and maternal gene interaction in the equine placenta. Proceedings of the National Academy of Sciences. 118(16):e2006474118. doi:10.1073/pnas.2006474118

Tangseefa P, Martin SK, Chin PY, Breen J, Mah CY, Baldock PA, Wittert GA, Page AJ, Proud CG, Fitter S & Zannettino ACW. (2021). The mTORC1 complex in pre-osteoblasts regulates whole-body energy metabolism independently of osteocalcin. Bone Research 9:10. doi:10.1038/s41413-020-00123-z

2020

Hng CH, 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. 10:11345. doi:10.1038/s41598-020-68261-2.

McClure BJ, Heatley SL, Rehn J, Breen J, Sutton R, Hughes TP, Suppiah R, Revesz T, Osborn M, White D, Yeung DT & White DL. (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:10.1111/bjh.17002

Breen J, McAninch D, Jankovic-Karasoulos T, McCullough D, Smith MD, Bogias KJ, Wan Q, Choudhry A, Hin N, Pederson SM, Bianco-Miotto T & Roberts CT. (2020). Temporal placental genome wide expression profiles reflect three phases of utero-placental blood flow during early to mid human gestation. MedRxiv. doi:10.1101/2020.06.25.20139709. PREPRINT

Brown CY, Sadlon TJ, Hope CM, Wong YY, Wong SW, Liu N, Withers H, Brown KA, Bandara V, Gundsambuu B, Pederson SM, Breen J, Robertson SA, Forrest A, Beyer M & Barry SC. (2020). Molecular Insights Into Regulatory T-Cell Adaptation to Self, Environment, and Host Tissues: Plasticity or Loss of Function in Autoimmune Disease. Frontiers of Immunology. 11:1269. doi:10.3389/fimmu.2020.01269

Kennedy S, Jarboui M-A, Srihari S, Raso C, Bryan K, Dernayka L, Charitou T, Bernal-Llinares M, Herrera-Montavez C, Krstic A, Matallanas D, Kotlyar M, Jurisica I, Curak J, Wong V, Stagljar I, LeBihan T, Imrie L, Pillai P, Lynn MA, Fasterius E, Szigyarto CA-K, Breen J, Kiel C, Serrano L, Rauch N, Rukhlenko O, Kholodenko BN, Iglesias-Martinez LF, Ryan C, Pilkington R, Cammareri P, Sansom O, Shave S, Auer M, Horn N, Klose F, Ueffing M, Boldt K, Lynn DJ & Kolch W. (2020). Extensive Rewiring of the the Epidermal Growth Factor Receptor EGFR Networks in Colorectal Cancer Cells Expressing Transforming Levels of Oncogenic KRAS G13D. Nature Communications. 11:499. doi:10.1038/s41467-019-14224-9

Singhal G, Morgan J, Jawahar MC, Corrigan F, Jaehne EJ, Toben C, Breen J, Pederson SM, Manavis J, Hannan AJ & Baune BT. (2020). Effects of aging on the motor, cognitive and affective behaviors, neuroimmune responses and hippocampal gene expression. Behavioural Brain Research. 383:112501. doi:10.1016/j.bbr.2020.112501

2019

Wan Q, Leemaqz SY, Pederson SM, McCullough D, McAninch DC, Jankovic-Karasoulos T, Smith MD, Bogias KJ, Liu N, Breen J, Roberts CT & Bianco-Miotto TM. (2019). Quality control measures for placental sample purity in DNA methylation array analyses. Placenta. 88: 8-11. doi:10.1016/j.placenta.2019.09.006.

Breen J & Rabanus-Wallace MT. (2019). New tricks for old wheat. Nature Plants. 5:1108–1109. doi:10.1038/s41477-019-0528-3. First Author/Invited Commentary

Kedzior SGE, Bianco-Miotto T, Breen J, Diener KR, Donnelley M, Dunning KR, Penno MAS, Schjenken JE, Sharkey DJ, Hodyl NA, Fullston T, Gardiner M, Brown HM & Rumbold AR. (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 & Society Online. doi:10.1016/j.rbms.2019.08.004.

Siggs OM, Souzeau E, Breen J, Qassim A, Zhou T, Dubowsky A, Ruddle JB & Craig JE. (2019). Autosomal dominant nanophthalmos and high hyperopia associated with a C-terminal MYRF frameshift variant. Molecular Vision. 25:527-534. PMID:31700225

Singhal G, Morgan J, Jawahar MC, Corrigan F, Jaehne EJ, Toben C, Breen J, Pederson SM, Hannan AJ & Baune BT. (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:10.3758/s13415-019-00743-x

Dinh DT, Breen J, Akison LK, DeMayo FJ, Brown HM, Robker RL & Russell DL. (2019). Characterization of progesterone receptor-chromatin binding properties and tissue-specific gene expression in mouse reproductive tissues. Scienific Reports. 9: 11966. doi:10.1038/s41598-019-48333-8.

Singhal G, Morgan J, Jawahar MC, Corrigan F, Jaehne EJ, Toben C, Breen J, Pederson SM, Hannan AJ & Baune BT. (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. doi:10.1016/j.bbr.2019.111917.

Weyrich L, Farrer A, Eisenhofer R, Arriola LA, YoungJ, Selway C, Handsley-Davis M, Adler CJ, Breen J & Cooper A. (2019). Laboratory contamination over time during low-biomass sample analysis. Molecular Ecology Resources. 19(4):982-996. doi:10.1111/1755-0998.13011 Preprint: bioRxiv https://www.biorxiv.org/content/10.1101/460212v1

Morgan J, Singhal G, Corrigan F, Jaehne EJ, Jawahar MC, Breen J, Pedersen S & Baune BT. (2019). Easing exercise induces depression-like, anxiety-like, and impaired cognitive-like behaviours and hippocampal dysfunction. Brain Research Bulletin. 148:118-130. doi:10.1016/j.brainresbull.2019.02.014.

Lim M, Brown HM, Kind KL, Breen J, Anastasi MR, Ritter LJ, Tregoweth EK, Dinh DT, Thompson JG, Dunning KR. (2019). Haemoglobin expression in in vivo murine preimplantation embryos suggests a role in oxygen-regulated gene expression. Reproduction, Fertility and Development. doi:10.1071/RD17321.

Hatzirodos N, Hummitzsch K, Irving-Rodgers HF, Breen J, Perry VEA, Anderson RA & Rodgers RJ. (2019). Transcript abundance of stromal and thecal cell-related genes during bovine ovarian development. PLOS One. 14(3): e0213575. doi:10.1371/journal.pone.0213575.

Crowe-Riddell JM, Simões BF, Partridge JC, Hunt DM, Delean S, Schwerdt JG, Breen J, Ludington A, Gower AJ & Sanders KLS. (2019). Phototactic tails: Evolution and molecular basis of a novel sensory trait in sea snakes. Molecular Ecology. 9(10): 2640. doi:10.1111/mec.15022.

2018

Tikhomirova A, Trappetti C, Standish A, Zhou Y, Breen J, Pederson S, Zilm P, Paton JC, 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. fty074. doi:10.1093/femspd/fty074.

Estrada O, Breen J, Richards SM & Cooper A. (2018). Ancient plant DNA in the genomic era. Nature Plants 4:394–396. doi:10.1038/s41477-018-0187-9. Corresponding/Senior Author

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. 7(2):e1011. doi:10.1002/cti2.1011.

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. 2190. doi:10.1038/s41598-018-19655-w. Corresponding/Senior Author

2017

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. 8:1860. doi:10.3389/fpls.2017.01860
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

2016

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

2015

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

2014

2013

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

2012

2011

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

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): 463-76. 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

2009

2008

2007

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

Consortium papers

Adam M. Bournazos, Lisa G. Riley, Shobhana Bommireddipalli, Lesley Ades, Lauren S. Akesson, Mohammad Al-Shinnag, Stephen I. Alexander, Alison D. Archibald, Shanti Balasubramaniam, Yemima Berman, Victoria Beshay, Kirsten Boggs, Jasmina Bojadzieva, Natasha J. Brown, Samantha J. Bryen, Michael F. Buckley, Belinda Chong, Mark R. Davis, Ruebena Dawes, Martin Delatycki, Liz Donaldson, Lilian Downie, Caitlin Edwards, Matthew Edwards, Amanda Engel, Lisa J. Ewans, Fathimath Faiz, Andrew Fennell, Michael Field, Mary-Louise Freckmann, Lyndon Gallacher, Russell Gear, Himanshu Goel, Shuxiang Goh, Linda Goodwin, Bernadette Hanna, James Harraway, Megan Higgins, Gladys Ho, Bruce K. Hopper, Ari E. Horton, Matthew F. Hunter, Aamira J. Huq, Sarah Josephi-Taylor, Himanshu Joshi, Edwin Kirk, Emma Krzesinski, Kishore R. Kumar, Frances Lemckert, Richard J. Leventer, Suzanna E. Lindsey-Temple, Sebastian Lunke, Alan Ma, Steven Macaskill, Amali Mallawaarachchi, Melanie Marty, Justine E. Marum, Hugh J. McCarthy, Manoj P. Menezes, Alison McLean, Di Milnes, Shekeeb Mohammad, David Mowat, Aram Niaz, Elizabeth E. Palmer, Chirag Patel, Shilpan G. Patel, Dean Phelan, Jason R. Pinner, Sulekha Rajagopalan, Matthew Regan, Jonathan Rodgers, Miriam Rodrigues, Richard H. Roxburgh, Rani Sachdev, Tony Roscioli, Ruvishani Samarasekera, Sarah A. Sandaradura, Elena Savva, Tim Schindler, Margit Shah, Ingrid B. Sinnerbrink, Janine M. Smith, Richard J. Smith, Amanda Springer, Zornitza Stark, Samuel P. Strom, Carolyn M. Sue, Kenneth Tan, Tiong Y. Tan, Esther Tantsis, Michel C. Tchan, Bryony A. Thompson, Alison H. Trainer, Karin van Spaendonck-Zwarts, Rebecca Walsh, Linda Warwick, Stephanie White, Susan M. White, Mark G. Williams, Meredith J. Wilson, Wui Kwan Wong, Dale C. Wright, Patrick Yap, Alison Yeung, Helen Young, Kristi J. Jones, Bruce Bennetts, Sandra T. Cooper, …, Jimmy Breen, … (2022). Standardized practices for RNA diagnostics using clinically accessible specimens reclassifies 75% of putative splicing variants. Genetics in Medicine. 24(1):130-145. doi:10.1016/j.gim.2021.09.001

Bournazos AM, Riley LG, Bommireddipalli S, Ades L, Akesson LS, Al-Shinnag M, Alexander SI, Archibald AD, Balasubramaniam S, Berman Y, et al. (2022). Standardized practices for RNA diagnostics using clinically accessible specimens reclassifies 75% of putative splicing variants. Genetics in Medicine. 24:130–145.

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.

Alaux M, Rogers J, Letellier T, Flores R, Alfama F, Pommier C, Mohellibi N, Durand S, Kimmel E, Michotey C, Guerche C, Loaec M, Lainé M, Steinbach D, Choulet F, Rimbert H, Leroy P, Guilhot N, Salse J, Feuillet C, International Wheat Genome Sequencing Consortium, Paux E, Eversole K, Adam-Blondon A-F and Quesneville H. (2018). Linking the International Wheat Genome Sequencing Consortium bread wheat reference genome sequence to wheat genetic and phenomic data. Genome Biology. 19:111. doi: 10.1186/s13059-018-1491-4

Book chapters

Estrada O, Richards SM & Breen J. (2021). Discovering the Secrets of Ancient Plants: Recovery of DNA from Museum and Archaeological Plant Specimens. In Pereira-Santana A, Gamboa-Tuz SD & Rodriguez-Zapata LC (eds.), Plant Comparative Genomics, Methods in Molecular Biology, vol. 2512, https://doi.org/10.1007/978-1-0716-2429-6_15

Grant Funding

Current

Completed

Professional Associations and Committees

Conferences Publications

Breen J, Smith MD, McAninch D, Jankovic-Karasoulos T, McCullough D, Pederson SM, Bogias KJ, Wan Q, Bianco-Miotto T & Roberts CT. (2020). Defining Co-expression Patterns and Molecular Pathways of the Placenta During Early Pregnancy. REPRODUCTIVE SCIENCES 27 (SUPPL 1), 251A-251A

Wan Q, Breen J, Leemaqz SYL, Pederson SM, Jankovic-Karasoulos T, McAninch D, McCullough D, Smith MD, Bogias KJ, Roberts CT. & Bianco-Miotto T. (2020). Characterisation of Placental DNA Methylation Across Early Human Gestation. REPRODUCTIVE SCIENCES 27 (SUPPL 1), 249A-249A.

Yeung DT, Greenwood M, Rhen J, Heatley SA, McClure B, Eadie LN, Breen J, Schutz C, Trahair TN, Wei AH, Dalla-Pozza L, Sutton R, Bradstock KF, Osborn MP & White CL. (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. Blood. 134(Supplement_1): 3949. doi:10.1182/blood-2019-127788.

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

Conference submissions (as presenting author)

Mayne BT, 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

Invited Presentations

2024 AGTA

2024 GA4GH

25-02-2021 Virtual Placenta-Interface Seminar Series University of Florida, USA.

2019 PLACENTAL GENE REGULATION IN EARLY GESTATION
ANZPRA satellite meeting, University of Newcastle, Newcastle NSW

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)

Other Media

2019 Inside the wonderous world of bioinformatics SAHMRI website (Inside the wonderous world of bioinformatics)

2019 Seeing Sea Snakes in a New Light Adelaide Advertiser (Seeing Sea Snakes in a New Light)

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)

Student Supervision

PhD

Current

Primary supervised in bold

Completed

MSc Biotechnology (All Primary Supervised)

Completed

BSc (honours)

Completed

Awards

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