Sung H, Ferlay J, Siegel RL, Laversanne M, Soerjomataram I, Jemal A, et al. Global cancer statistics 2020: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries. CA Cancer J Clin. 2021;71:209–49.
de Visser KE, Joyce JA. The evolving tumor microenvironment: from cancer initiation to metastatic outgrowth. Cancer Cell. 2023;41:374–403.
Brasel K, De Smedt T, Smith JL, Maliszewski CR. Generation of murine dendritic cells from flt3-ligand-supplemented bone marrow cultures. Blood. 2000;96:3029–39.
Article CAS PubMed Google Scholar
McKenna HJ, Stocking KL, Miller RE, Brasel K, De Smedt T, Maraskovsky E, et al. Mice lacking flt3 ligand have deficient hematopoiesis affecting hematopoietic progenitor cells, dendritic cells, and natural killer cells. Blood. 2000;95:3489–97.
Article CAS PubMed Google Scholar
Barry KC, Hsu J, Broz ML, Cueto FJ, Binnewies M, Combes AJ, et al. A natural killer-dendritic cell axis defines checkpoint therapy-responsive tumor microenvironments. Nat Med. 2018;24:1178–91.
Article CAS PubMed PubMed Central Google Scholar
Li S, Zhang N, Zhang H, Yang Z, Cheng Q, Wei K, et al. Deciphering the role of LGALS2: insights into tertiary lymphoid structure-associated dendritic cell activation and immunotherapeutic potential in breast cancer patients. Mol Cancer. 2024;23:216.
Article CAS PubMed PubMed Central Google Scholar
Zhang N, Zhang H, Li S, Wu W, Luo P, Liu Z, et al. Uncovering the predictive and immunomodulatory potential of transient receptor potential melastatin family-related CCNE1 in pan-cancer. Mol Cancer. 2024;23:258.
Article CAS PubMed PubMed Central Google Scholar
Hla DA, Hindin DI. Generative AI & machine learning in surgical education. Curr Probl Surg. 2025;63:101701.
Skov RAC, Lawaetz J, Strom M, Van Herzeele I, Konge L, Resch TA, et al. Machine learning enhances assessment of proficiency in endovascular aortic repair simulations. Curr Probl Surg. 2024;61:101576.
Zhang H, Lin C, Chen Y, Shen X, Wang R, Chen Y, et al. Enhancing molecular network-based cancer driver gene prediction using machine learning approaches: current challenges and opportunities. J Cell Mol Med. 2025;29:e70351.
Article PubMed PubMed Central Google Scholar
Morabito S, Reese F, Rahimzadeh N, Miyoshi E, Swarup V. Hdwgcna identifies co-expression networks in high-dimensional transcriptomics data. Cell Rep Methods. 2023;3:100498.
Article CAS PubMed PubMed Central Google Scholar
Papanicolaou M, Parker AL, Yam M, Filipe EC, Wu SZ, Chitty JL, et al. Temporal profiling of the breast tumour microenvironment reveals collagen XII as a driver of metastasis. Nat Commun. 2022;13:4587.
Article CAS PubMed PubMed Central Google Scholar
Satija R, Farrell JA, Gennert D, Schier AF, Regev A. Spatial reconstruction of single-cell gene expression data. Nat Biotechnol. 2015;33:495–502.
Article CAS PubMed PubMed Central Google Scholar
Korsunsky I, Millard N, Fan J, Slowikowski K, Zhang F, Wei K, et al. Fast, sensitive and accurate integration of single-cell data with harmony. Nat Methods. 2019;16:1289–96.
Article CAS PubMed PubMed Central Google Scholar
Barbie DA, Tamayo P, Boehm JS, Kim SY, Moody SE, Dunn IF, et al. Systematic RNA interference reveals that oncogenic KRAS-driven cancers require TBK1. Nature. 2009;462:108–12.
Article CAS PubMed PubMed Central Google Scholar
Dalal H, Dahlgren M, Gladchuk S, Brueffer C, Gruvberger-Saal SK, Saal LH. Clinical associations of ESR2 (estrogen receptor beta) expression across thousands of primary breast tumors. Sci Rep. 2022;12:4696.
Article CAS PubMed PubMed Central Google Scholar
Jezequel P, Kerdraon O, Hondermarck H, Guerin-Charbonnel C, Lasla H, Gouraud W, et al. Identification of three subtypes of triple-negative breast cancer with potential therapeutic implications. Breast Cancer Res. 2019;21:65.
Article PubMed PubMed Central Google Scholar
Liberzon A, Birger C, Thorvaldsdottir H, Ghandi M, Mesirov JP, Tamayo P. The molecular signatures database (MSigDB) hallmark gene set collection. Cell Syst. 2015;1:417–25.
Article CAS PubMed PubMed Central Google Scholar
Aibar S, Gonzalez-Blas CB, Moerman T, Huynh-Thu VA, Imrichova H, Hulselmans G, et al. SCENIC: single-cell regulatory network inference and clustering. Nat Methods. 2017;14:1083–6.
Article CAS PubMed PubMed Central Google Scholar
Ishwaran H, Kogalur UB, Blackstone EH, Lauer MS. Random survival forests. Ann Appl Stat. 2008;2:841–60.
De Bin R. Boosting in Cox regression: a comparison between the likelihood-based and the model-based approaches with focus on the R-packages CoxBoost and mboost. Comput Stat. 2016;31:513–31.
Maeser D, Gruener RF, Huang RS. oncoPredict: an R package for predicting in vivo or cancer patient drug response and biomarkers from cell line screening data. Brief Bioinform. 2021. https://doi.org/10.1093/bib/bbab260.
Article PubMed PubMed Central Google Scholar
Becht E, Giraldo NA, Lacroix L, Buttard B, Elarouci N, Petitprez F, et al. Estimating the population abundance of tissue-infiltrating immune and stromal cell populations using gene expression. Genome Biol. 2016;17:218.
Article PubMed PubMed Central Google Scholar
Charoentong P, Finotello F, Angelova M, Mayer C, Efremova M, Rieder D, et al. Pan-cancer immunogenomic analyses reveal genotype-immunophenotype relationships and predictors of response to checkpoint blockade. Cell Rep. 2017;18:248–62.
Article CAS PubMed Google Scholar
Davoli T, Uno H, Wooten EC, Elledge SJ. Tumor aneuploidy correlates with markers of immune evasion and with reduced response to immunotherapy. Science. 2017. https://doi.org/10.1126/science.aaf8399.
Article PubMed PubMed Central Google Scholar
Thorsson V, Gibbs DL, Brown SD, Wolf D, Bortone DS, Ou Yang TH, et al. The immune landscape of cancer. Immunity. 2018;48:812–30.
Article CAS PubMed PubMed Central Google Scholar
Zhang N, Yang M, Yang JM, Zhang CY, Guo AY. A predictive network-based immune checkpoint blockade immunotherapeutic signature optimizing patient selection and treatment strategies. Small Methods. 2024;8:e2301685.
Rooney MS, Shukla SA, Wu CJ, Getz G, Hacohen N. Molecular and genetic properties of tumors associated with local immune cytolytic activity. Cell. 2015;160:48–61.
Article CAS PubMed PubMed Central Google Scholar
Ayers M, Lunceford J, Nebozhyn M, Murphy E, Loboda A, Kaufman DR, et al
Comments (0)