Dr James (Jim) Blackburn

Dr James Blackburn is Group Leader for the DNA and RNA Methodologies group within the Translational Oncology Laboratory. Originally from the UK, he has extensive experience and expertise in method development and implementation across a broad range of research disciplines. After gaining a degree in
Senior Research Officer

Conjoint/Adjunct Role(s)

Conjoint Senior Lecturer, UNSW Medicine

Dr James Blackburn is Group Leader for the DNA and RNA Methodologies group within the Translational Oncology Laboratory. Originally from the UK, he has extensive experience and expertise in method development and implementation 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 Division as a founding member of both the Genome Evolution (2010) and the Transcriptomic Research (2014) groups. Now within the Cancer Division and leading his own team, Dr Blackburn's current research focus is three-fold:

1) The clinical establishment of two singular assays for fusion gene detection in blood cancers and solid tumours (based on targeted RNA sequencing)

2) The deployment of a targeted sequencing approach to enhance Next Generation Sequencing methods in clinical research

3) The development of new methodologies to improve sequencing libraries generated from formalin-fixed tissues

Research Interests

Cancer genetics / epigenetics
Genome evolution and adaptation
Embryogenesis, evolution and development

Awards and Honours

Winner of the Choong-Dickinson Best Poster Award at the 2018 ASSG / ASG Annual Scientific Meeting
Winner of the ABCAM Best Poster at the 2016 5th Annual Garvan Post Doctoral Symposium


2004 – PhD Human Molecular Genetics, University of London (Imperial College) - UK
2000 – BSc (Hons) Genetics, University of Manchester - UK

Selected Publications

Nagai, T., Trakanant, S., Kawasaki, M., Kawasaki, K., Watanabe, M., Blackburn, J., et al. 2019. The microRNAs control eyelid development through regulating Wnt signaling. Dev. Dyn. (Accepted)

Heyer, E.E., Deveson, I.W., Wooi, D., Selinger, C.I., ... et al. ... Mercer, T.R.*, Blackburn, J*. 2018. Diagnosis of fusion genes using targeted RNA sequencing. Nat. Commun. (Accepted)

Blackburn, J.*, Wong, T.*, Kanakamedala, B.S., Barker, C., Hardwick, S.A., et al. 2018. Using DNA spike-in controls (sequins) with human genome sequencing. Nat. Protoc. (Accepted)

Ishikawa, R., Porntaveetus, T., Kawasaki, K., Kawasaki, M., Blackburn, J., et al. 2018. Lrp4/Wise regulates palatal rugae development through Turing-type reaction-diffusion mechanisms. PLOS One 13(9):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(6):e1700731 

Hardwick, S.A., Chen, W.Y., Wong, T., Deveson, I.W., Blackburn, J., Andersen, S.B., Nielsen, L.K., Mattick, J.S., Mercer, T.R. 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

Person portrait

Dr James (Jim) Blackburn

Research group