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Socrates: identification of genomic rearrangements in tumour genomes by re-aligning soft clipped reads.
Schröder J, Hsu A, Boyle SE, Macintyre G, Cmero M, Tothill RW, Johnstone RW, Shackleton M, Papenfuss AT. Schröder J, et al. Among authors: papenfuss at. Bioinformatics. 2014 Apr 15;30(8):1064-1072. doi: 10.1093/bioinformatics/btt767. Epub 2014 Jan 2. Bioinformatics. 2014. PMID: 24389656 Free PMC article.
Socrates has single-nucleotide resolution, identifies micro-homologies and untemplated sequence at break points, has high sensitivity and high specificity and takes advantage of parallelism for efficient use of resources. ...AVAILABILITY AND IMPLEMENTATION: Socrates is rel …
Socrates has single-nucleotide resolution, identifies micro-homologies and untemplated sequence at break points, has high sensitivity …
HYSYS: have you swapped your samples?
Schröder J, Corbin V, Papenfuss AT. Schröder J, et al. Among authors: papenfuss at. Bioinformatics. 2017 Feb 15;33(4):596-598. doi: 10.1093/bioinformatics/btw685. Bioinformatics. 2017. PMID: 28003257 Free PMC article.
The collection and analysis of cancer sequencing data in the clinical setting is an elaborate process that may involve consenting patients, obtaining possibly-multiple DNA samples, sequencing and analysis. Many of these steps are manual. At any stage mistakes can occur tha …
The collection and analysis of cancer sequencing data in the clinical setting is an elaborate process that may involve consenting patients, …
Two of a kind: transmissible Schwann cell cancers in the endangered Tasmanian devil (Sarcophilus harrisii).
Patchett AL, Coorens THH, Darby J, Wilson R, McKay MJ, Kamath KS, Rubin A, Wakefield M, Mcintosh L, Mangiola S, Pye RJ, Flies AS, Corcoran LM, Lyons AB, Woods GM, Murchison EP, Papenfuss AT, Tovar C. Patchett AL, et al. Among authors: papenfuss at. Cell Mol Life Sci. 2020 May;77(9):1847-1858. doi: 10.1007/s00018-019-03259-2. Epub 2019 Aug 2. Cell Mol Life Sci. 2020. PMID: 31375869 Free PMC article.
Combined BRAF, MEK, and CDK4/6 Inhibition Depletes Intratumoral Immune-Potentiating Myeloid Populations in Melanoma.
Lelliott EJ, Mangiola S, Ramsbottom KM, Zethoven M, Lim L, Lau PKH, Oliver AJ, Martelotto LG, Kirby L, Martin C, Patel RP, Slater A, Cullinane C, Papenfuss AT, Haynes NM, McArthur GA, Oliaro J, Sheppard KE. Lelliott EJ, et al. Among authors: papenfuss at. Cancer Immunol Res. 2021 Feb;9(2):136-146. doi: 10.1158/2326-6066.CIR-20-0401. Epub 2020 Dec 10. Cancer Immunol Res. 2021. PMID: 33303574
VIRUSBreakend: Viral Integration Recognition Using Single Breakends.
Cameron DL, Jacobs N, Roepman P, Priestley P, Cuppen E, Papenfuss AT. Cameron DL, et al. Among authors: papenfuss at. Bioinformatics. 2021 Oct 11;37(19):3115-3119. doi: 10.1093/bioinformatics/btab343. Bioinformatics. 2021. PMID: 33973999 Free PMC article.
Interfacing Seurat with the R tidy universe.
Mangiola S, Doyle MA, Papenfuss AT. Mangiola S, et al. Among authors: papenfuss at. Bioinformatics. 2021 Nov 18;37(22):4100-4107. doi: 10.1093/bioinformatics/btab404. Bioinformatics. 2021. PMID: 34028547 Free PMC article.
191 results