Dr Jim Blackburn
Biography
Dr Jim Blackburn is Group Leader for the DNA and RNA Methodologies team within the Genomic Cancer Medicine Laboratory. Originally from the UK, he has extensive experience and expertise across a broad range of research disciplines.
After gaining a degree in genetics from the University of Manchester, Dr Blackburn undertook postgraduate studies in the molecular genetics underlying human blindness at Imperial College London. He followed this with a postdoctoral fellow position at King's College London researching the molecular and developmental genetics that influence and guide tooth, palate, tongue and eyelid formation. It was during this time that Dr Blackburn gained an interest in combining his developmental research with that of palaeontology and field biology disciplines (EvoDevo).
Based on his combined scientific interests and research experience, Dr Blackburn was recruited to the Garvan Institute in 2010, joining the Genomics and Epigenetics Research Theme as a founding member of both the Genome Evolution Laboratory (2010) and the Transcriptomic Research Laboratory (2014).
Leading his own team within the Cancer Research Theme since 2019, Dr Blackburn's current research focus is three-fold:
1) Leading the Garvan-based sequencing for the Molecular Screening and Therapeutics (MoST) clinical program of Omico Australia
2) Developing and deploying unique sequencing assays for comprehensive fusion gene detection in blood cancers and solid tumours
3) Developing innovative methods and novel approaches to enhance next-generation sequencing capabilities
Dr Jim Blackburn is Group Leader for the DNA and RNA Methodologies team within the Genomic Cancer Medicine Laboratory. Originally from the UK, he has extensive experience and expertise across a broad range of research disciplines.
After gaining a degree in genetics from the University of Manchester, Dr Blackburn undertook postgraduate studies in the molecular genetics underlying human blindness at Imperial College London. He followed this with a postdoctoral fellow position at King's College London researching the molecular and developmental genetics that influence and guide tooth, palate, tongue and eyelid formation. It was during this time that Dr Blackburn gained an interest in combining his developmental research with that of palaeontology and field biology disciplines (EvoDevo).
Based on his combined scientific interests and research experience, Dr Blackburn was recruited to the Garvan Institute in 2010, joining the Genomics and Epigenetics Research Theme as a founding member of both the Genome Evolution Laboratory (2010) and the Transcriptomic Research Laboratory (2014).
Leading his own team within the Cancer Research Theme since 2019, Dr Blackburn's current research focus is three-fold:
1) Leading the Garvan-based sequencing for the Molecular Screening and Therapeutics (MoST) clinical program of Omico Australia
2) Developing and deploying unique sequencing assays for comprehensive fusion gene detection in blood cancers and solid tumours
3) Developing innovative methods and novel approaches to enhance next-generation sequencing capabilities
Awards and Honours
Winner of the ABCAM Best Poster at the 2016 5th Annual Garvan Post Doctoral Symposium
Education
2000 – BSc (Hons) Genetics, University of Manchester - UK
Fundings
Blackburn, J. Improving Fusion Gene Detection and Immune Response Assessment in Sarcoma Patients. ANZSA Research Grant 2020
Blackburn, J. Improving Sarcoma Cancer Diagnostics Through Implementation of a Novel Fusion Gene Test. NFMRI Research Grant, 2020-2021.
Blackburn, J., Heyer, E.E., Trahair, T.N. Accurately Diagnosing Fusion Genes in Paediatric and Adolescent and Young Adult (AYA) Sarcomas. St. Vincent’s Clinic Foundation Research Grant, 2019.
Mercer, T.R., Dinger, M.E., Burnett, L., Blackburn, J. Diagnosis of Inherited Genetic Disorders Using DNA Reference Standards. NHMRC Project Grant, 2018-2020.
Mercer, T.R., Gill, D., Blackburn, J. A Universal Clinical Test for Gene Fusions in Blood Cancer. NHMRC Project Grant, 2016-2018.
Selected Publications
Vargas, A.C., Heyer, E.E., Cheah, A.L., Bonar, F., Jones, M., Maclean, F.M., Gill, A.J., Blackburn, J. 2023. A novel NEAT1-GLI1 translocation identified in unclassified soft tissue sarcomas of young individuals by hybridisation capture sequencing of RNA. Pathology (In Press) [https://doi.org/10.1016/j.pathol.2022.11.012]
Bartonicek, N., Rouet, R., Warren, J., Loetsch, C., Rodriguez, G.S., ... ... ... Blackburn, J., et al. 2022. The retroelement Lx9 puts a brake on the immune response to virus infection. Nature 608:757-765
Bournazos, A.M., Riley, L.G., Bommireddipalli, S., Ades, L., Akesson, L.S., ... ... ... Australasian Consortium for RNA Diagnostics. 2022. Standardized practices for RNA diagnostics using clinically accessible specimens reclassifies 75% of putative splicing variants. Genet. Med. 24:130-145
Whiteley, S.L., Holleley, C.E., Wagner, S., Blackburn, J., Deveson, I.W., et al. 2021. Two transcriptionally distinct pathways drive female development in a reptile with both genetic and temperature dependent sex determination. PLoS Genet. 17:e1009465
Gong, B., Li, D., Kusko, R., Novoradovskaya, N., Zhang, Y., ... ... ... Blackburn, J., et al. 2021. Cross-oncopanel study reveals high sensitivity and accuracy with overall analytical performance depending on genomic regions. Genome Biol. 22:109
Deveson, I.W., Gong, B., Lai, K., LoCoco, J.S., Richmond, T.A., ... ... ... Blackburn, J., et al. 2021. Evaluating the analytical validity of circulating tumor DNA sequencing for precision oncology. Nat. Biotechnol. 39:1115-1128
Mueller, S.A., Gauthier, M.E.A., Blackburn, J., Grady, J.P., Kraitsek, S., et al. 2020. Molecular patterns in salivary duct carcinoma identify prognostic subgroups. Mod. Pathol. 33:1896-1909
Yamada, A., Kawasaki, M., Miake, Y., Yamada, Y., Blackburn, J., et al. 2020. Overactivation of the NF-kB pathway impairs molar enamel formation. Oral Dis. 26:1513-1522
Reis, A.L.M., Deveson, I.W., Wong, T., Madala, B.S., Barker, C., Blackburn, J., et al. 2020. A universal and independent synthetic DNA ladder for the quantitative measurement of genomic features. Nat. Commun. 11:3609
Heyer, E.E., Blackburn, J. 2020. Sequencing strategies for fusion gene detection. BioEssays 42:e2000016
Singh, M., Jackson, K.J.L., Wang, J.J., Schofield, P., Field, M.A., ... ... ... Blackburn, J., et al. 2020. Lymphoma driver mutations in the pathogenic evolution of an iconic human autoantibody. Cell 180:878-894
Singh, M.*, Al-Eryani, G.*, Carswell, S., Ferguson, J.M., Blackburn, J., et al. 2019. High-throughput targeted long-read single cell sequencing reveals the clonal and transcriptional landscape of lymphocytes. Nat. Commun. 10:3120
Blackburn, J.*, Wong, T.*, Kanakamedala, B.S., Barker, C., Hardwick, S.A., et al. 2019. Use of synthetic DNA spike-in controls (sequins) for human genome sequencing. Nat. Protoc. 14:2119-2151
Trahair, T.N., Gifford, A.J., Fordham, A., Mayoh, C., Fadia, M., ... ... ... Blackburn, J., et al. 2019. Crizotinib and surgery for long term disease control in children and adolescents with ALK-positive inflammatory myofibroblastic tumors. JCO Precis. Oncol. 3:1-11
Blackburn, J., Vecchiarelli, S., Heyer, E.E., Patrick, S.M., Lyons, R.J., et al. 2019. TMPRSS2-ERG fusions linked to prostate cancer racial health disparities: A focus on Africa. Prostate 79:1191-1196
Heyer, E.E., Deveson, I.W., Wooi, D., Selinger, C.I., ... et al. ... Mercer, T.R.*, Blackburn, J*. 2019. Diagnosis of fusion genes using targeted RNA sequencing. Nat. Commun. 10:1388
Hardwick, S.A.*, Bassett, S.D.*, Kaczorowski, D.C., Blackburn, J., Barton, K.M., et al. 2019. Targeted, high-resolution RNA sequencing of non-coding genomic regions associated with neuropsychiatric functions. Front. Genet. 10:309
Deveson, I.W.*, Madala, B.S.*, Blackburn, J., Barker, C., Wong, T., et al. 2019. Chiral DNA sequences as commutable controls for clinical genomics. Nat. Commun. 10:1342
Nagai, T., Trakanant, S., Kawasaki, M., Kawasaki, K., Yamada, Y., Watanabe, M., Blackburn, J., et al. 2019. MicroRNAs control eyelid development through regulating Wnt signaling. Dev. Dyn. 248:201-210
Kawasaki, M.*, Kawasaki, K.*, Meguro, F., Yamada, A., Ishikawa, R., Porntaveetus, T., Blackburn, J., et al. 2018. Lrp4/Wise regulates palatal rugae development through Turing-type reaction-diffusion mechanisms. PLOS One 13:e0204126
Deveson, I.W.*, Brunck, M.E.*, Blackburn, J., Tseng, E., Hon, T., et al. 2018. Universal alternative splicing of noncoding exons. Cell Systems 6:245-255
Fleuren, E.D.G, Vlenterie, M., van der Graaf, W.T.A., Hillebrandt-Roeffen, M.H.S., Blackburn, J., et al. 2017. Phosphoproteomic profiling across sarcoma subtypes reveals ALK and MET as novel actionable targets in synovial sarcomas. Cancer Res. 77:4279-4292
Deveson, I.W.*, Holleley, C.E.*, Blackburn, J., Marshall Graves, J.A., Mattick, J.S., et al. 2017. Differential intron retention in Jumonji chromatin modifier genes is implicated in reptile temperature-dependent sex determination. Sci. Adv. 3:e1700731
Hardwick, S.A.*, Chen, W.Y.*, Wong, T., Deveson, I.W., Blackburn, J., et al. 2016. Spliced synthetic genes as internal controls in RNA sequencing experiments. Nat. Methods 13:792-798
Kawasaki, M., Kawasaki, K., Oommen, S., Blackburn, J., et al. 2016. Regional regulation of filiform tongue papillae development by Ikka/Irf6. Dev. Dyn. 245:937-46
Watanabe, M.*, Kawasaki, K.*, Kawasaki, M., Portaveetus, T., Oommen, S., Blackburn, J., et al. 2016. Spatio-temporal expression of Sox genes in murine palatogenesis. Gene Expr. Patterns 21:111-118
Blackburn, J., Roden, D.L., Ng, R., Wu, J., Bosman, A., Epstein, R.J. 2016. Damage-inducible intragenic demethylation of the human TP53 tumor suppressor gene is associated with transcription from an alternative intronic promoter. Mol. Carcinog. 55:1940-1951
Blackburn, J.*, Kawasaki, K.*, Porntaveetus, T.*, Kawasaki, M., Otsuka-Tanaka, Y., et al. 2015. Excess NF-kB induces ectopic odontogenesis in embryonic incisor epithelium. J. Dent. Res. 94:121-128
Kawasaki, K.*, Porntaveetus, T.*, Oommen, S., Ghafoor, S., Kawasaki, M., Otsuka-Tanaka, Y., Blackburn, J., et al. 2012. Bmp signalling in filiform tongue papillae development. Arch. Oral Biol. 57:805-813
Blackburn, J., Ohazama, A., Kawasaki, K., Otsuka-Tanaka, Y., Liu, B., et al. 2012. The role of Irf6 in tooth epithelial invagination. Dev. Biol. 365:61-70
Ohazama, A., Blackburn, J., Porntaveetus, T., Ota, M.S., Choi, H., et al. 2010. A role for suppressed incisor cuspal morphogenesis in the evolution of mammalian heterodont dentition. PNAS 107:92-97
Ohazama, A., Haycraft, C.J., Seppala, M., Blackburn, J., Ghafoor, S., et al. 2009. Primary cilia regulate Shh activity in the control of molar tooth number. Development. 136:897–903
Matalová, E., Setková, J., Blackburn, J., Mísek, I., Sharpe, P.T. 2006. CD 95 mediated apoptosis in embryogenesis: implication in tooth development. Orthod. Craniofacial Res. 9:123–128
Courtney, J-M., Blackburn, J., Sharpe, P.T. 2005. The Ectodysplasin and NFkB signalling pathways in odontogenesis. Arch. Oral Biol. 50:159–163
Blackburn, J., Tarttelin, E.E., Gregory-Evans, C.Y., Moosajee, M., Gregory-Evans, K. 2003. Transcriptional Regulation and Expression of the Dominant Drusen Gene FBLN3 (EFEMP1) in Mammalian Retina. Invest. Ophthalmol. Vis. Sci. 44:4613-4621
Tarttelin, E.E., Gregory-Evans, C.Y., Bird, A.C., Weleber, R.G., Klein, M.L., Blackburn, J., Gregory-Evans, K. 2001. Molecular genetic heterogeneity in autosomal dominant drusen. J. Med. Genet. 38:381–384
