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About

My research spans bioinformatics methods development and computational cancer biology. My team and I have developed advanced methods for detection of genomic rearrangements using short read sequencing technology and methods for multiomics data analysis. We’ve applied these in a wide range of projects that have been either collaborative or that we have driven ourselves. Major areas of research include performing the first genome project for an Australian marsupial, mapping the genome of the scabies mite, uncovering the tissue of origin of the contagious Tasmanian Facial Devil Tumour, identifying the catastrophic process underlying cancer neo chromosome formation, and evolution of advanced melanoma.

Publications

Selected publications from Prof Tony Papenfuss

Al Kamran Khan A, Wu J, Sun Y, Barrow AD, Papenfuss AT, Mangiola S. cellsig plug-in enhances CIBERSORTx signature selection for multidataset transcriptomes with sparse multilevel modelling. Bioinformatics. 2023;39(12):10.1093/bioinformatics/btad685

Mangiola S, Roth-Schulze AJ, Trussart M, Zozaya-Valdés E, Ma M, Gao Z, Rubin AF, Speed TP, Shim H, Papenfuss AT. sccomp: Robust differential composition and variability analysis for single-cell data. Proceedings of the National Academy of Sciences of the United States of America. 2023;120(33):10.1073/pnas.2203828120

Giner G, Ikram S, Herold MJ, Papenfuss AT. A systematic review of computational methods for designing efficient guides for CRISPR DNA base editor systems. Briefings in Bioinformatics. 2023;24(4):10.1093/bib/bbad205

Molania R, Foroutan M, Gagnon-Bartsch JA, Gandolfo LC, Jain A, Sinha A, Olshansky G, Dobrovic A, Papenfuss AT, Speed TP. Removing unwanted variation from large-scale RNA sequencing data with PRPS. Nature Biotechnology. 2023;41(1):10.1038/s41587-022-01440-w

Cameron DL, Dong R, Papenfuss AT. StructuralVariantAnnotation: a R/Bioconductor foundation for a caller-agnostic structural variant software ecosystem. Bioinformatics. 2022;38(7):10.1093/bioinformatics/btac042

Dong R, Cameron D, Bedo J, Papenfuss AT. svaRetro and svaNUMT: modular packages for annotating retrotransposed transcripts and nuclear integration of mitochondrial DNA in genome sequencing data. Gigabyte. 2022;2022:10.46471/gigabyte.70

Mangiola S, Doyle MA, Papenfuss AT. Interfacing Seurat with the R tidy universe. Bioinformatics. 2021;37(22):10.1093/bioinformatics/btab404

Cameron DL, Jacobs N, Roepman P, Priestley P, Cuppen E, Papenfuss AT. VIRUSBreakend: Viral Integration Recognition Using Single Breakends. Bioinformatics. 2021;37(19):10.1093/bioinformatics/btab343

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 Biology. 2021;22(1):10.1186/s13059-021-02423-x

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 S-J, McArthur GA, Mann GJ, Levesque MP, Papenfuss AT, Shackleton M. Evolution of late-stage metastatic melanoma is dominated by aneuploidy and whole genome doubling. Nature Communications. 2021;12(1):10.1038/s41467-021-21576-8

Lab research projects

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