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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 …
The architecture and evolution of cancer neochromosomes.
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. Garsed DW, et al. Among authors: papenfuss at. Cancer Cell. 2014 Nov 10;26(5):653-67. doi: 10.1016/j.ccell.2014.09.010. Epub 2014 Nov 10. Cancer Cell. 2014. PMID: 25517748 Free article.
Genomic characterisation of Eμ-Myc mouse lymphomas identifies Bcor as a Myc co-operative tumour-suppressor gene.
Lefebure M, Tothill RW, Kruse E, Hawkins ED, Shortt J, Matthews GM, Gregory GP, Martin BP, Kelly MJ, Todorovski I, Doyle MA, Lupat R, Li J, Schroeder J, Wall M, Craig S, Poortinga G, Cameron D, Bywater M, Kats L, Gearhart MD, Bardwell VJ, Dickins RA, Hannan RD, Papenfuss AT, Johnstone RW. Lefebure M, et al. Among authors: papenfuss at. Nat Commun. 2017 Mar 6;8:14581. doi: 10.1038/ncomms14581. Nat Commun. 2017. PMID: 28262675 Free PMC article.
Circulating tumour DNA reflects treatment response and clonal evolution in chronic lymphocytic leukaemia.
Yeh P, Hunter T, Sinha D, Ftouni S, Wallach E, Jiang D, Chan YC, Wong SQ, Silva MJ, Vedururu R, Doig K, Lam E, Arnau GM, Semple T, Wall M, Zivanovic A, Agarwal R, Petrone P, Jones K, Westerman D, Blombery P, Seymour JF, Papenfuss AT, Dawson MA, Tam CS, Dawson SJ. Yeh P, et al. Among authors: papenfuss at. Nat Commun. 2017 Mar 17;8:14756. doi: 10.1038/ncomms14756. Nat Commun. 2017. PMID: 28303898 Free PMC article.
Corrigendum: Whole genome analysis of a schistosomiasis-transmitting freshwater snail.
Adema CM, Hillier LW, Jones CS, Loker ES, Knight M, Minx P, Oliveira G, Raghavan N, Shedlock A, do Amaral LR, Arican-Goktas HD, Assis JG, Baba EH, Baron OL, Bayne CJ, Bickham-Wright U, Biggar KK, Blouin M, Bonning BC, Botka C, Bridger JM, Buckley KM, Buddenborg SK, Lima Caldeira R, Carleton J, Carvalho OS, Castillo MG, Chalmers IW, Christensens M, Clifton S, Cosseau C, Coustau C, Cripps RM, Cuesta-Astroz Y, Cummins SF, Di Stefano L, Dinguirard N, Duval D, Emrich S, Feschotte C, Feyereisen R, FitzGerald P, Fronick C, Fulton L, Galinier R, Gava SG, Geusz M, Geyer KK, Giraldo-Calderón GI, de Souza Gomes M, Gordy MA, Gourbal B, Grunau C, Hanington PC, Hoffmann KF, Hughes D, Humphries J, Jackson DJ, Jannotti-Passos LK, de Jesus Jeremias W, Jobling S, Kamel B, Kapusta A, Kaur S, Koene JM, Kohn AB, Lawson D, Lawton SP, Liang D, Limpanont Y, Liu S, Lockyer AE, Lovato TAL, Ludolf F, Magrini V, McManus DP, Medina M, Misra M, Mitta G, Mkoji GM, Montague MJ, Montelongo C, Moroz LL, Munoz-Torres MC, Niazi U, Noble LR, Oliveira FS, Pais FS, Papenfuss AT, Peace R, Pena JJ, Pila EA, Quelais T, Raney BJ, Rast JP, Rollinson D, Rosse IC, Rotgans B, Routledge EJ, Ryan KM, Scholte LLS, Storey K… See abstract for full author list ➔ Adema CM, et al. Among authors: papenfuss at. Nat Commun. 2017 Aug 23;8:16153. doi: 10.1038/ncomms16153. Nat Commun. 2017. PMID: 28832025 Free PMC article.
187 results