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- Education
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- 3D and 4D imaging of thymic T cell differentiation
- Activating https://www.wehi.edu.au/node/add/individual-student-research-page#Parkin to treat Parkinson’s disease
- Activation, regulation, and biological roles of E3 ubiquitin ligases
- Bioinformatics methods for detecting and making sense of somatic genomic rearrangements
- Characterising regulatory T cells in coeliac disease
- Computational melanoma genomics
- Deep profiling of blood cancers during targeted therapy
- Defining the role of necroptosis in platelet production and function
- Determining the migration signals leading to protective immune responses
- Developing mucolytics to treat chronic respiratory diseases
- Developing new tools to visualise necroptotic cell death
- Development of live-cell, automated microscopy techniques for studying malaria
- Development of tools to inform malaria vaccine design
- Discovering new genetic causes of primary antibody deficiencies
- Discovery of novel drug combinations for the treatment of bowel cancer
- Dissecting the induction and integration of T cell migration cues
- Drug targets and compounds that block growth of malaria parasites
- Effects of nutrition on immunity and infection in Asia and Africa
- Eosinophil and neutrophil heterogeneity
- Eosinophil maturation
- Epigenetic regulation of systemic iron homeostasis
- Functional differences between young and old platelets
- Generation of cytokine antagonists
- Genetic dissection of mechanisms of Plasmodium invasion
- Genomic characterisation of epigenetic regulators involved in X inactivation
- High resolution 3-dimensional imaging to characterise metastatic cancers
- High-resolution imaging of host cell invasion by the malaria parasite
- Home renovations: understanding how Toxoplasma redecorates its host cell
- How the epigenetic regulator SMCHD1 works and how to target it to treat disease
- Human monoclonal antibodies against malaria infection
- Identification of malaria parasite entry receptors
- Identification of new therapeutic opportunities for pancreatic cancer
- Identifying disease-causing haplotypes with hidden Markov models
- Interleukin-11 in gastrointestinal bacterial infections
- Investigating mechanisms of cell death and survival using zebrafish
- Investigating new paths to selective modulation of potassium channels
- Let me in! How Toxoplasma invades human cells
- Long-read sequencing for transcriptome and epigenome analysis
- Macro-evolution in cancer
- Mapping DNA repair networks in cancer
- Mapping how multiple malaria episodes are related
- Modelling gene regulatory systems
- Modulation of immune responses by immunosuppressive chemokines
- Molecular basis for inherited Parkinson’s disease mechanism of PINK1
- Mucus at the molecular level
- Novel cell death and inflammatory modulators in lupus
- Plasmodium vivax host-parasite interactions: impact on immunity
- Predicting drug response in cancer
- Programming T cells to defend against infections
- Reconstructing the immune response: from molecules to cells to systems
- Regulation of cytokine signalling
- Screening for regulators of jumping genes
- Target identification of potent antimalarial agents
- Targeting the immune system in cancer
- The role of interleukin-11 in acute myeloid leukaemia
- Transmembrane control of type I cytokine receptor activation
- Uncovering the roles of long non-coding RNAs in human bowel cancer
- Understanding retinal eye diseases with retinal transcriptomic data analysis
- Understanding the role of stromal cells in pancreatic cancer growth
- Unravelling the tumour suppressor network in models of lung cancer
- Utilising pre-clinical models to discover novel therapies for tuberculosis
- Zombieland: evolution of a dead enzyme that kills cells by necroptosis
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Tony Papenfuss-Publications
Researcher:
Selected publications
- Garsed DW*, Marshall OJ*, Corbin VDA*, Hsu A*, Di Stefano L, Schröder J, Li J, Feng Z-P, Kim BW, Kowarsky M, Lansdell B, Brookwell R, Myklebost O, Meza-Zepeda L, Holloway AJ, Pedeutour F, Choo KHA, Damore MA, J. DA, Papenfuss AT**, Thomas DM**. Architecture and Evolution of a Cancer Neochromosome. Cancer Cell (accepted 8/2014).
- Schroder J*, Hsu A*, Boyle SE, Macintyre G, Cmero M, Tothill RW, Johnstone RW, Shackleton M, Papenfuss AT. Socrates: identification of genomic rearrangements in tumour genomes by re-aligning soft clipped reads. Bioinformatics. 2014 Jan 22. PMID: 24389656.
- Mar VJ*, Wong SQ*, Li J, Scolyer RA, McLean C, Papenfuss AT, Tothill RW, Kakavand H, Mann GJ, Thompson JF, Behren A, Cebon JS, Wolfe R, Kelly JW, Dobrovic A, McArthur GA, BRAF/NRAS wild-type melanomas have a high mutation load correlating with histological and molecular signatures of UV damage. Clinical Cancer Research 2013, 19(17); 1–10. PMID: 23833303
- Murchison EP, Tovar C, Hsu A, Bender HS, Kheradpour P, Rebbeck CA, Obendorf D, Conlan C, Bahlo M, Blizzard CA, Pyecroft S, Kreiss A, Kellis M, Stark A, Harkins TT, Marshall Graves JA, Woods GM, Hannon GJ, Papenfuss AT. The Tasmanian devil transcriptome reveals Schwann cell origins of a clonally transmissible cancer. Science. 2010 Jan 1;327(5961):84-7. PMID: 20044575.
- Baum J*, Papenfuss AT*, Mair GR*, Janse CJ*, Vlachou D, Waters AP, Cowman AF, Crabb BS, de Koning-Ward TF. Molecular genetics and comparative genomics reveal RNAi is not functional in malaria parasites. Nucleic Acids Res. 2009 Jun;37(11):3788-98. PMID: 19380379.
- Warren WC, Hillier LW, Marshall Graves JA, Birney E, Ponting CP, Grutzner F, Belov K, Miller W, Clarke L, Chinwalla AT, Yang SP, Heger A, Locke DP, Miethke P, Waters PD, Veyrunes F, Fulton L, Fulton B, Graves T, Wallis J, Puente XS, Lopez-Otin C, Ordonez GR, Eichler EE, Chen L, Cheng Z, Deakin JE, Alsop A, Thompson K, Kirby P, Papenfuss AT, Wakefield MJ, Olender T, Lancet D, Huttley GA, Smit AF, Pask A, Temple-Smith P, Batzer MA, Walker JA, Konkel MK, Harris RS, Whittington CM, Wong ES, Gemmell NJ, Buschiazzo E, Vargas Jentzsch IM, Merkel A, Schmitz J, Zemann A, Churakov G, Kriegs JO, Brosius J, Murchison EP, Sachidanandam R, Smith C, Hannon GJ, Tsend-Ayush E, McMillan D, Attenborough R, Rens W, Ferguson-Smith M, Lefevre CM, Sharp JA, Nicholas KR, Ray DA, Kube M, Reinhardt R, Pringle TH, Taylor J, Jones RC, Nixon B, Dacheux JL, Niwa H, Sekita Y, Huang X, Stark A, Kheradpour P, Kellis M, Flicek P, Chen Y, Webber C, Hardison R, Nelson J, Hallsworth-Pepin K, Delehaunty K, Markovic C, Minx P, Feng Y, Kremitzki C, Mitreva M, Glasscock J, Wylie T, Wohldmann P, Thiru P, Nhan MN, Pohl CS, Smith SM, Hou S, Nefedov M, de Jong PJ, Renfree MB, Mardis ER, Wilson RK. Genome analysis of the platypus reveals unique signatures of evolution. Nature. 2008 May 8;453(7192):175-83. PMID: 18464734.
- Mikkelsen TS, Wakefield MJ, Aken B, Amemiya CT, Chang JL, Duke S, Garber M, Gentles AJ, Goodstadt L, Heger A, Jurka J, Kamal M, Mauceli E, Searle SM, Sharpe T, Baker ML, Batzer MA, Benos PV, Belov K, Clamp M, Cook A, Cuff J, Das R, Davidow L, Deakin JE, Fazzari MJ, Glass JL, Grabherr M, Greally JM, Gu W, Hore TA, Huttley GA, Kleber M, Jirtle RL, Koina E, Lee JT, Mahony S, Marra MA, Miller RD, Nicholls RD, Oda M, Papenfuss AT, Parra ZE, Pollock DD, Ray DA, Schein JE, Speed TP, Thompson K, VandeBerg JL, Wade CM, Walker JA, Waters PD, Webber C, Weidman JR, Xie X, Zody MC, Broad Institute Genome Sequencing P, Broad Institute Whole Genome Assembly T, Graves JA, Ponting CP, Breen M, Samollow PB, Lander ES, Lindblad-Toh K. Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences. Nature. 2007 May 10;447(7141):167-77. PMID: 17495919.
- Belov K, Sanderson CE, Deakin JE, Wong ES, Assange D, McColl KA, Gout A, de Bono B, Barrow AD, Speed TP, Trowsdale J, Papenfuss AT. Characterization of the opossum immune genome provides insights into the evolution of the mammalian immune system. Genome Res. 2007 Jul;17(7):982-91. PMID: 17495011.
- Belov K, Deakin JE, Papenfuss AT, Baker ML, Melman SD, Siddle HV, Gouin N, Goode DL, Sargeant TJ, Robinson MD, Wakefield MJ, Mahony S, Cross JG, Benos PV, Samollow PB, Speed TP, Graves JA, Miller RD. Reconstructing an ancestral mammalian immune supercomplex from a marsupial major histocompatibility complex. PLoS Biol. 2006 Mar;4(3):e46. PMID: 16435885.
- Baum J*, Papenfuss AT*, Baum B, Speed TP, Cowman AF. Regulation of apicomplexan actin-based motility. Nat Rev Microbiol. 2006 Aug;4(8):621-8. PMID: 16845432.
* joint first authors
** joint last/corresponding authors