Google Scholar: https://scholar.google.com/citations?user=C9LOhrwAAAAJ&hl=en
Selected publications
Daniel L Cameron, Nina Jacobs, Paul Roepman, Peter Priestley, Edwin Cuppen, Anthony T Papenfuss, VIRUSBreakend: Viral Integration Recognition Using Single Breakends, Bioinformatics. 2021 May 11;btab343
Mangiola S, Molania R, Dong R, Doyle MA, Papenfuss AT. tidybulk: an R tidy framework for modular transcriptomic data analysis. Genome Biol. 2021 Jan 22;22(1):42.
Vergara IA, Mintoff CP, Sandhu S, McIntosh L, Young RJ, Wong SQ, Colebatch A, Cameron DL, Kwon JL, Wolfe R, Peng A, Ellul J, Dou X, Fedele C, Boyle S, Arnau GM, Raleigh J, Hatzimihalis A, Szeto P, Mooi J, Widmer DS, Cheng PF, Amann V, Dummer R, Hayward N, Wilmott J, Scolyer RA, Cho RJ, Bowtell D, Thorne H, Alsop K, Cordner S, Woodford N, Leditschke J, O’Brien P, Dawson SJ, McArthur GA, Mann GJ, Levesque MP, Papenfuss AT*, Shackleton M*. Evolution of late-stage metastatic melanoma is dominated by aneuploidy and whole genome doubling. Nat Commun. 2021 Mar 4;12(1):1434.
Bedő J, Di Stefano L, Papenfuss AT. Unifying package managers, workflow engines, and containers: Computational reproducibility with BioNix. Gigascience. 2020 Nov 18;9(11):giaa121.
Cameron DL, Di Stefano L, Papenfuss AT. Comprehensive evaluation and characterisation of short read general-purpose structural variant calling software. Nat Commun. 2019 Jul 19;10(1):3240
Tonkin-Hill GQ, Trianty L, Noviyanti R, Nguyen HHT, Sebayang BF, Lampah DA, Marfurt J, Cobbold SA, Rambhatla JS, McConville MJ, Rogerson SJ, Brown GV, Day KP, Price RN, Anstey NM, Papenfuss AT*, Duffy MF*. The Plasmodium falciparum transcriptome in severe malaria reveals altered expression of genes involved in important processes including surface antigen-encoding var genes. PLoS Biol. 2018 Mar 12;16(3):e2004328. (* Contributed equally)
Cameron DL, Schröder J, Penington JS, Do H, Molania R, Dobrovic A, Speed TP, Papenfuss AT. GRIDSS: sensitive and specific genomic rearrangement detection using positional de Bruijn graph assembly. Genome Res. 2017 Dec;27(12):2050-2060
Schroeder J, Corbin V, Papenfuss AT; HYSYS: Have you swapped your samples?, Bioinformatics 2016, Dec 6 btw685.
Mofiz E, Holt DC, Seemann T, Currie BJ, Fischer K*, and Papenfuss AT*; Genomic resources and draft assemblies of the human and porcine varieties of scabies mites, Sarcoptes scabiei var. hominis and var. suis, Gigascience 2016, 5:23.
Mofiz E, Seemann T, Bahlo M, Holt D, Currie BJ, Fischer K, Papenfuss AT; The mitochondrial genome sequence of the scabies mite provides insight into the genetic diversity of individual scabies infections, PLOS Neglected Tropical Diseases 2016, 10(2):e0004384
Colebatch AJ, Di Stefano L, Wong SQ, Hannan RD, Waring PM, Dobrovic A, McArthur GA*, Papenfuss AT*; Clustered somatic mutations are frequent in transcription factor binding motifs within proximal promoter regions in melanoma and other cutaneous malignancies. Oncotarget. 2016 Sep
Papenfuss AT, Feng Z-P, Krasnec K, Deakin JE, Baker ML, Miller RD, Marsupials and monotremes possess a novel family of MHC class I genes that is lost from the eutherian lineage, BMC Genomics 2015, Jul 22;16(1):535 (PMID: 26194104)
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, Deans AJ, Papenfuss AT**, Thomas DM**, Architecture and Evolution of a Cancer Neochromosome, Cancer Cell 2014 Nov 10;26(5):653-67 (* joint first authors; ** joint last/corresponding authors) (PMID: 25517748)
Schroeder 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, 30:8, 1064-1072. (* joint first authors)
Renfree MB*, Papenfuss AT*, Deakin JE, Lindsay J, Heider T, Belov K, Rens W, Waters PD, Pharo EA, Shaw G, Wong ES, Lefevre CM, Nicholas KR, Kuroki Y, Wakefield MJ, Zenger KR, Wang C, Ferguson-Smith M, Nicholas FW, Hickford D, Yu H, Short KR, Siddle HV, Frankenberg SR, Chew KY, Menzies BR, Stringer JM, Suzuki S, Hore TA, Delbridge ML, Mohammadi A, Schneider NY, Hu Y, O’Hara W, Al Nadaf S, Wu C, Feng ZP, Cocks BG, Wang J, Flicek P, Searle SM, Fairley S, Beal K, Herrero J, Carone DM, Suzuki Y, Sagano S, Toyoda A, Sakaki Y, Kondo S, Nishida Y, Tatsumoto S, Mandiou I, Hsu A, McColl KA, Landsell B, Weinstock G, Kuczek E, McGrath A, Wilson P, Men A, Hazar-Rethinam M, Hall A, Davies J, Wood D, Williams S, Sundaravadanam Y, Muzny DM, Jhangiani SN, Lewis LR, Morgan MB, Okwuonu GO, Ruiz SJ, Santibanez J, Nazareth L, Cree A, Fowler G, Kovar CL, Dinh HH, Joshi V, Jing C, Lara F, Thornton R, Chen L, Deng J, Liu Y, Shen JY, Song XZ, Edson J, Troon C, Thomas D, Stephens A, Yapa L, Levchenko T, Gibbs RA, Cooper DW, Speed TP, Fujiyama A, Graves JA, O’Neill RJ, Pask AJ, Forrest SM, Worley KC. Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development, Genome Biology. 2011 Aug 19;12(8):R81. *Joint first & corresponding authors.
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 and Papenfuss AT, The Tasmanian devil transcriptome reveals Schwann cell origins of a clonally transmissible cancer, Science 2010, vol. 327 (5961) pp. 84-87.