Tony Papenfuss-Publications

Tony Papenfuss-Publications

Selected publications

Computational Cancer Biology

1.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. PMID: 33664264

2.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 Oct 11;7(41):66569-66585. PMID: 27611953

3.Garsed DW*, Marshall OJ*, Corbin VD*, Hsu A*, Di Stefano L, Schröder J, Li J, Feng ZP, Kim BW, Kowarsky M, Lansdell B, Brookwell R, Myklebost O, Meza-Zepeda L, Holloway AJ, Pedeutour F, Choo KH, Damore MA, Deans AJ, Papenfuss AT**, Thomas DM**. The architecture and evolution of cancer neochromosomes. Cancer Cell. 2014 Nov 10;26(5):653-67. PMID: 25517748

4.Fong CY, Gilan O, Lam EY, Rubin AF, Ftouni S, Tyler D, Stanley K, Sinha D, Yeh P, Morison J, Giotopoulos G, Lugo D, Jeffrey P, Lee SC, Carpenter C, Gregory R, Ramsay RG, Lane SW, Abdel-Wahab O, Kouzarides T, Johnstone RW, Dawson SJ, Huntly BJ, Prinjha RK, Papenfuss AT, Dawson MA. BET inhibitor resistance emerges from leukaemia stem cells. Nature. 2015 Sep 24;525(7570):538-42. PMID: 26367796

5.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

Genomic Rearrangement Detection Methods

6.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. PMID: 33973999

7.Cameron DL, Baber J, Shale C, Valle-Inclan JE, Besselink N, van Hoeck A, Janssen R, Cuppen E, Priestley P, Papenfuss AT. GRIDSS2: comprehensive characterisation of somatic structural variation using single breakend variants and structural variant phasing.Genome Biol. 2021 Jul 12;22(1):202. PMID: 34253237

8.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. PMID: 31324872

9.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. PMID: 29097403


Other bioinformatics methods

10.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. PMID: 33482892


* joint first authors; ** joint last/corresponding authors