Dr Tony Papenfuss
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Division: Bioinformatics
Research Overview
The human genome project and similar projects in disease-causing organisms such as Plasmodium falciparum, which causes malaria in humans, have provided new tools for discovery in biology and have accelerated the development of understanding in human disease. Recently, new sequencing technologies have made possible the collection of data from experiments at an unprecedented rate. This has made the analysis of high-throughput sequence data a critical part of biomedical research.
We work in the area of biological sequence analysis. We apply mathematics, statistics and computational methods to analyse genome, gene transcript and protein sequence data to provide new insights into diseases. A major focus of our group is the development of new methods to analyse short read sequence data from next generation sequencing platforms. We apply these methods to improve the understanding of diseases such as cancer and malaria.
We have also worked on several genome projects and a secondary focus of our group is the use of sequence data from multiple species to learn about the evolution of genes related to disease. This area is called computational comparative genomics. It is also the basis of approaches to sensitive genome searching that we have developed and applied to study genes in malaria and to discover novel genes in mammalian genomes.
Research Interests
- Analysis of Next Generation sequence data in cancer
- Methods for analysis of structural variation in cancer genomes
- Next Generation sequencing in malaria
- Computational comparative genomics
- Sensitive genomic sequence search techniques using hidden Markov models
- Tasmanian devil facial tumour disease
Selected Publications
- Murchison E, 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, Graves JA, Woods GM, Hannon GJ, Papenfuss AT. The Tasmanian Devil Transcriptome Reveals Schwann Cell Origins of a Clonally Transmissible Cancer, Science (2010) vol. 327 (5961) pp. 84-87. PMID: 20044575 [PubMed - in process]
- Baum J*, Papenfuss AT*, Mair GR*, Janse CJ, Waters AP, Cowman AF, Crabb BS, de Koning-Ward TF. Molecular genetics and comparative genomics suggests RNAi is not functional in malaria parasites, Nucleic Acids Research 2009 Jun;37(11):3788-98. (* joint first authors) PMID: 19380379 [PubMed - indexed for MEDLINE]
- Baum J*, Papenfuss AT*, Baum B, Speed TP, Cowman AF. Regulation of Apicomplexan actin-based motility, Nature Reviews Microbiology 4, 621-628 (August). (* joint first authors) PMID: 16845432 [PubMed - indexed for MEDLINE]
- de Koning-Ward TF, Gilson PR, Boddey JA, Rug M, Smith BJ, Papenfuss AT, Sanders PR, Lundie RJ, Maier AG, Cowman AF, Crabb BS. A newly discovered protein export machine in malaria parasites, Nature 2009, 459(7249):945-9. PMID: 19536257 [PubMed - indexed for MEDLINE]
- Scott AM, Lee FT, Jones R, Hopkins W, MacGregor D, Cebon JS, Hannah A, Chong G, U P, Papenfuss A, Rigopoulos A, Sturrock S, Murphy R, Wirth V, Murone C, Smyth FE, Knight S, Welt S, Ritter G, Richards E, Nice EC, Burgess AW, Old LJ. A Phase I Trial of Humanized Monoclonal Antibody A33 in Patients with Colorectal Carcinoma: Biodistribution, Pharmacokinetics, and Quantitative Tumor Uptake, Clinical Cancer Research 2005;11 4810-4817. PMID: 16000578 [PubMed - indexed for MEDLINE]
- K Belov, CE Sanderson, JE Deakin, ESW Wong, D Assange, KA McColl, A Gout, B de Bono, TP Speed, J Trowsdale, AT Papenfuss. Characterization of the opossum immune genome provides insights into the evolution of the mammalian immune system, Genome Research, 17:982-991, 2007. PMID: 18463304 [PubMed - indexed for MEDLINE]
- 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 MHC, PLoS Biology, 2006, 4(3): e46
- Warren W, Hillier LW, Marshall Graves JA, Birney E, Ponting CP, Grützner F, Belov K, Miller W, Clarke L, Chinwalla AT, Yang SP, Heger A, Locke D, Miethke P, Waters PD, Veyrunes F, Fulton L, Fulton B, Graves T, Wallis J, Puente XS, López-Otín C, Ordóñez G, 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 PD, Batzer MA, Walker JA, Konkel M, Harris R, Whittington C, Wong ES, Gemmell N, Buschiazzo E, Vargas Jentzsch I, Merkel A, Schmitz J, Zemann A, Churakov G, Kriegs JO, Brosius J, Murchison E, Sachidanandam R, Smith C, Hannon GJ, Tsend-Ayush E, Mcmillan D, Attenborough R, Rens W, Ferguson-Smith M, Lefèvre C, Sharp J, Nicholas K, Ray DA, Kube M, Reinhardt R, Pringle T, Taylor J, Jones R, Nixon B, Dacheux J, 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 S, Hou S, 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 [PubMed - indexed for MEDLINE]
- 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 Platform, Broad Institute Whole Genome Assembly Team, Baldwin J, Abdouelleil A, Abdulkadir J, Abebe A, Abera B, Abreu J, Acer SC, Aftuck L, Alexander A, An P, Anderson E, Anderson S, Arachi H, Azer M, Bachantsang P, Barry A, Bayul T, Berlin A, Bessette D, Bloom T, Boguslavskiy L, Bonnet C, Boukhgalter B, Bourzgui I, Brown A, Cahill P, Channer S, Cheshatsang Y, Chuda L, Citroen M, Collymore A, Cooke P, Costello M, D'Aco K, Daza R, De Haan G, DeGray S, DeMaso C, Dhargay N, Dooley K, Dooley E, Doricent M, Dorje P, Dorjee K, Dupes A, Elong R, Falk J, Farina A, Faro S, Ferguson D, Fisher S, Foley CD, Franke A, Friedrich D, Gadbois L, Gearin G, Gearin CR, Giannoukos G, Goode T, Graham J, Grandbois E, Grewal S, Gyaltsen K, Hafez N, Hagos B, Hall J, Henson C, Hollinger A, Honan T, Huard MD, Hughes L, Hurhula B, Husby ME, Kamat A, Kanga B, Kashin S, Khazanovich D, Kisner P, Lance K, Lara M, Lee W, Lennon N, Letendre F, LeVine R, Lipovsky A, Liu X, Liu J, Liu S, Lokyitsang T, Lokyitsang Y, Lubonja R, Lui A, MacDonald P, Magnisalis V, Maru K, Matthews C, McCusker W, McDonough S, Mehta T, Meldrim J, Meneus L, Mihai O, Mihalev A, Mihova T, Mittelman R, Mlenga V, Montmayeur A, Mulrain L, Navidi A, Naylor J, Negash T, Nguyen T, Nguyen N, Nicol R, Norbu C, Norbu N, Novod N, O'Neill B, Osman S, Markiewicz E, Oyono OL, Patti C, Phunkhang P, Pierre F, Priest M, Raghuraman S, Rege F, Reyes R, Rise C, Rogov P, Ross K, Ryan E, Settipalli S, Shea T, Sherpa N, Shi L, Shih D, Sparrow T, Spaulding J, Stalker J, Stange-Thomann N, Stavropoulos S, Stone C, Strader C, Tesfaye S, Thomson T, Thoulutsang Y, Thoulutsang D, Topham K, Topping I, Tsamla T, Vassiliev H, Vo A, Wangchuk T, Wangdi T, Weiand M, Wilkinson J, Wilson A, Yadav S, Young G, Yu Q, Zembek L, Zhong D, Zimmer A, Zwirko Z, Jaffe DB, Alvarez P, Brockman W, Butler J, Chin C, Gnerre S, MacCallum I, 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, Vol 447, 10 May 2007. PMID: 17495919 [PubMed - indexed for MEDLINE]
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Current Laboratory Members
Faculty Member: Tony Papenfuss, BSc(Hons) PhD Mon
Postdoctoral Fellow: Arthur Hsu, BA BE PhD Melb
Postdoctoral Fellow: Vincent Corbin, BS Florida MS PhD Montana
Research assistant: Mark Kowarsky, BSc Melb
Research assistant: Jan Schroeder
Research assistant: Chris Davoren, BEng QUT
Masters student: Ehtesham Mofiz, BS Dhaka
UROP student: Lachlan Mcintosh
Administrative Officer: Maria Markovic, BA RMIT DipEd LaTrobe
