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DeMixSC: a deconvolution framework that uses single-cell sequencing plus a small benchmark dataset for improved analysis of cell-type ratios in complex tissue samples.
Guo S, Liu X, Cheng X, Jiang Y, Ji S, Liang Q, Koval A, Li Y, Owen LA, Kim IK, Aparicio A, Shen JP, Kopetz S, Weinstein JN, DeAngelis MM, Chen R, Wang W. Guo S, et al. bioRxiv [Preprint]. 2023 Nov 11:2023.10.10.561733. doi: 10.1101/2023.10.10.561733. bioRxiv. 2023. PMID: 37873318 Free PMC article. Preprint.
Validating risk prediction models for multiple primaries and competing cancer outcomes in families with Li-Fraumeni syndrome using clinically ascertained data at a single institute.
Nguyen NH, Dodd-Eaton EB, Corredor JL, Woodman-Ross J, Green S, Hernandez ND, Gutierrez Barrera AM, Arun BK, Wang W. Nguyen NH, et al. medRxiv [Preprint]. 2023 Sep 2:2023.08.31.23294849. doi: 10.1101/2023.08.31.23294849. medRxiv. 2023. PMID: 37693464 Free PMC article. Updated. Preprint.
TP53 gain-of-function mutation modulates the immunosuppressive microenvironment in non-HPV-associated oral squamous cell carcinoma.
Shi Y, Ren X, Cao S, Chen X, Yuan B, Brasil da Costa FH, Rodriguez Rosario AE, Corona A, Michikawa C, Veeramachaneni R, Osman AA, Xie T, Wang W, Sikora AG, Myers JN, Rangel R. Shi Y, et al. J Immunother Cancer. 2023 Aug;11(8):e006666. doi: 10.1136/jitc-2023-006666. J Immunother Cancer. 2023. PMID: 37604640 Free PMC article.
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. 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.
Single-cell ATAC and RNA sequencing reveal pre-existing and persistent cells associated with prostate cancer relapse.
Taavitsainen S, Engedal N, Cao S, Handle F, Erickson A, Prekovic S, Wetterskog D, Tolonen T, Vuorinen EM, Kiviaho A, Nätkin R, Häkkinen T, Devlies W, Henttinen S, Kaarijärvi R, Lahnalampi M, Kaljunen H, Nowakowska K, Syvälä H, Bläuer M, Cremaschi P, Claessens F, Visakorpi T, Tammela TLJ, Murtola T, Granberg KJ, Lamb AD, Ketola K, Mills IG, Attard G, Wang W, Nykter M, Urbanucci A. Taavitsainen S, et al. Nat Commun. 2021 Sep 6;12(1):5307. doi: 10.1038/s41467-021-25624-1. Nat Commun. 2021. PMID: 34489465 Free PMC article.
17 results