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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: salim a. Nat Med. 2018 Jul;24(7):986-993. doi: 10.1038/s41591-018-0078-7. Epub 2018 Jun 25. Nat Med. 2018. PMID: 29942092
Publisher Correction: 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: salim a. Nat Med. 2018 Dec;24(12):1941. doi: 10.1038/s41591-018-0176-6. Nat Med. 2018. PMID: 30135555
RUV-III-NB: normalization of single cell RNA-seq data.
Salim A, Molania R, Wang J, De Livera A, Thijssen R, Speed TP. Salim A, et al. Nucleic Acids Res. 2022 Sep 9;50(16):e96. doi: 10.1093/nar/gkac486. Nucleic Acids Res. 2022. PMID: 35758618 Free PMC article.
Feasibility of reusing time-matched controls in an overlapping cohort.
Delcoigne B, Hagenbuch N, Schelin ME, Salim A, Lindström LS, Bergh J, Czene K, Reilly M. Delcoigne B, et al. Among authors: salim a. Stat Methods Med Res. 2018 Jun;27(6):1818-1829. doi: 10.1177/0962280216669744. Epub 2016 Sep 21. Stat Methods Med Res. 2018. PMID: 27659169
Powerful differential expression analysis incorporating network topology for next-generation sequencing data.
Dona MSI, Prendergast LA, Mathivanan S, Keerthikumar S, Salim A. Dona MSI, et al. Among authors: salim a. Bioinformatics. 2017 May 15;33(10):1505-1513. doi: 10.1093/bioinformatics/btw833. Bioinformatics. 2017. PMID: 28172447
Simulation studies demonstrate that our method outperforms the two-state MRF model for various sample sizes. Furthermore, for a comparable FDR, it has better sensitivity than DESeq, EBSeq, edgeR and NOISeq. ...After installation, type vignette("pathDESeq") to access the vi …
Simulation studies demonstrate that our method outperforms the two-state MRF model for various sample sizes. Furthermore, for a compa …
1,186 results