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Page 1
Estimation of tumor cell total mRNA expression in 15 cancer types predicts disease progression.
Cao S, Wang JR, Ji S, Yang P, Dai Y, Guo S, Montierth MD, Shen JP, Zhao X, Chen J, Lee JJ, Guerrero PA, Spetsieris N, Engedal N, Taavitsainen S, Yu K, Livingstone J, Bhandari V, Hubert SM, Daw NC, Futreal PA, Efstathiou E, Lim B, Viale A, Zhang J, Nykter M, Czerniak BA, Brown PH, Swanton C, Msaouel P, Maitra A, Kopetz S, Campbell P, Speed TP, Boutros PC, Zhu H, Urbanucci A, Demeulemeester J, Van Loo P, Wang W. Cao S, et al. Among authors: speed tp. Nat Biotechnol. 2022 Nov;40(11):1624-1633. doi: 10.1038/s41587-022-01342-x. Epub 2022 Jun 13. Nat Biotechnol. 2022. PMID: 35697807 Free PMC article.
SRMA: an R package for resequencing array data analysis.
Zhang N, Xu Y, O'Hely M, Speed TP, Scharfe C, Wang W. Zhang N, et al. Among authors: speed tp. Bioinformatics. 2012 Jul 15;28(14):1928-30. doi: 10.1093/bioinformatics/bts286. Epub 2012 May 10. Bioinformatics. 2012. PMID: 22581181 Free PMC article.
Removing unwanted variation from large-scale RNA sequencing data with PRPS.
Molania R, Foroutan M, Gagnon-Bartsch JA, Gandolfo LC, Jain A, Sinha A, Olshansky G, Dobrovic A, Papenfuss AT, Speed TP. Molania R, et al. Among authors: speed tp. Nat Biotechnol. 2023 Jan;41(1):82-95. doi: 10.1038/s41587-022-01440-w. Epub 2022 Sep 15. Nat Biotechnol. 2023. PMID: 36109686 Free PMC article.
International network of cancer genome projects.
International Cancer Genome Consortium; Hudson TJ, Anderson W, Artez A, Barker AD, Bell C, Bernabé RR, Bhan MK, Calvo F, Eerola I, Gerhard DS, Guttmacher A, Guyer M, Hemsley FM, Jennings JL, Kerr D, Klatt P, Kolar P, Kusada J, Lane DP, Laplace F, Youyong L, Nettekoven G, Ozenberger B, Peterson J, Rao TS, Remacle J, Schafer AJ, Shibata T, Stratton MR, Vockley JG, Watanabe K, Yang H, Yuen MM, Knoppers BM, Bobrow M, Cambon-Thomsen A, Dressler LG, Dyke SO, Joly Y, Kato K, Kennedy KL, Nicolás P, Parker MJ, Rial-Sebbag E, Romeo-Casabona CM, Shaw KM, Wallace S, Wiesner GL, Zeps N, Lichter P, Biankin AV, Chabannon C, Chin L, Clément B, de Alava E, Degos F, Ferguson ML, Geary P, Hayes DN, Hudson TJ, Johns AL, Kasprzyk A, Nakagawa H, Penny R, Piris MA, Sarin R, Scarpa A, Shibata T, van de Vijver M, Futreal PA, Aburatani H, Bayés M, Botwell DD, Campbell PJ, Estivill X, Gerhard DS, Grimmond SM, Gut I, Hirst M, López-Otín C, Majumder P, Marra M, McPherson JD, Nakagawa H, Ning Z, Puente XS, Ruan Y, Shibata T, Stratton MR, Stunnenberg HG, Swerdlow H, Velculescu VE, Wilson RK, Xue HH, Yang L, Spellman PT, Bader GD, Boutros PC, Campbell PJ, Flicek P, Getz G, Guigó R, Guo G, Haussler D, Heath S, Hu… See abstract for full author list ➔ International Cancer Genome Consortium, et al. Among authors: speed tp. Nature. 2010 Apr 15;464(7291):993-8. doi: 10.1038/nature08987. Nature. 2010. PMID: 20393554 Free PMC article.
The Subclonal Architecture of Metastatic Breast Cancer: Results from a Prospective Community-Based Rapid Autopsy Program "CASCADE".
Savas P, Teo ZL, Lefevre C, Flensburg C, Caramia F, Alsop K, Mansour M, Francis PA, Thorne HA, Silva MJ, Kanu N, Dietzen M, Rowan A, Kschischo M, Fox S, Bowtell DD, Dawson SJ, Speed TP, Swanton C, Loi S. Savas P, et al. Among authors: speed tp. PLoS Med. 2016 Dec 27;13(12):e1002204. doi: 10.1371/journal.pmed.1002204. eCollection 2016 Dec. PLoS Med. 2016. PMID: 28027312 Free PMC article.
Single-cell profiling of breast cancer T cells reveals a tissue-resident memory subset associated with improved prognosis.
Savas P, Virassamy B, Ye C, Salim A, Mintoff CP, Caramia F, Salgado R, Byrne DJ, Teo ZL, Dushyanthen S, Byrne A, Wein L, Luen SJ, Poliness C, Nightingale SS, Skandarajah AS, Gyorki DE, Thornton CM, Beavis PA, Fox SB; Kathleen Cuningham Foundation Consortium for Research into Familial Breast Cancer (kConFab); Darcy PK, Speed TP, Mackay LK, Neeson PJ, Loi S. Savas P, et al. Among authors: speed tp. Nat Med. 2018 Jul;24(7):986-993. doi: 10.1038/s41591-018-0078-7. Epub 2018 Jun 25. Nat Med. 2018. PMID: 29942092
Spatial analysis with SPIAT and spaSim to characterize and simulate tissue microenvironments.
Feng Y, Yang T, Zhu J, Li M, Doyle M, Ozcoban V, Bass GT, Pizzolla A, Cain L, Weng S, Pasam A, Kocovski N, Huang YK, Keam SP, Speed TP, Neeson PJ, Pearson RB, Sandhu S, Goode DL, Trigos AS. Feng Y, et al. Among authors: speed tp. Nat Commun. 2023 May 15;14(1):2697. doi: 10.1038/s41467-023-37822-0. Nat Commun. 2023. PMID: 37188662 Free PMC article.
271 results