Hausser J, Alon U. Tumour heterogeneity and the evolutionary trade-offs of cancer. Nature Rev Cancer. 2020;20:247–57.

Article  CAS  Google Scholar 

Rashkin SR, Graff RE, Kachuri L, Thai KK, Alexeeff SE, Blatchins MA, et al. Pan-cancer study detects genetic risk variants and shared genetic basis in two large cohorts. Nature Commun. 2020;11:4423.

Article  CAS  Google Scholar 

Chen F, Wendl MC, Wyczalkowski MA, Bailey MH, Li Y, Ding L. Moving pan-cancer studies from basic research toward the clinic. Nat Cancer. 2021;2:879–90.

Article  PubMed  Google Scholar 

Coulton A, Murai J, Qian D, Thakkar K, Lewis CE, Litchfield K. Using a pan-cancer atlas to investigate tumour associated macrophages as regulators of immunotherapy response. Nat Commun. 2024;15:5665.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Conti A, Duggento A, Indovina I, Guerrisi M, Toschi N. Radiomics in breast cancer classification and prediction. Seminars cancer Biol. 2021;72:238–50.

Article  CAS  Google Scholar 

He Y, Duan S, Wang W, Yang H, Pan S, Cheng W, et al. Integrative radiomics clustering analysis to decipher breast cancer heterogeneity and prognostic indicators through multiparametric MRI. NPJ breast cancer. 2024;10:72.

Article  PubMed  PubMed Central  Google Scholar 

Liu Z, Duan T, Zhang Y, Weng S, Xu H, Ren Y, et al. Radiogenomics: a key component of precision cancer medicine. Br J Cancer. 2023;129:741–53.

Article  PubMed  PubMed Central  Google Scholar 

Fan M, Xia P, Clarke R, Wang Y, Li L. Radiogenomic signatures reveal multiscale intratumour heterogeneity associated with biological functions and survival in breast cancer. Nature Commun. 2020;11:4861.

Article  CAS  Google Scholar 

Wang S, Liu Z, Rong Y, Zhou B, Bai Y, Wei W, et al. Deep learning provides a new computed tomography-based prognostic biomarker for recurrence prediction in high-grade serous ovarian cancer. Radiother Oncol. 2019;132:171–7.

Article  PubMed  Google Scholar 

Wu J, Li C, Gensheimer M, Padda S, Kato F, Shirato H, et al. Radiological tumor classification across imaging modality and histology. Nat Mach Intell. 2021;3:787–98.

Article  PubMed  PubMed Central  Google Scholar 

Yue P, Lopez-Tapia F, Paladino D, Li Y, Chen CH, Namanja AT, et al. Hydroxamic Acid and Benzoic Acid-Based STAT3 Inhibitors Suppress Human Glioma and Breast Cancer Phenotypes In Vitro and In Vivo. Cancer Res. 2016;76:652–63.

Article  CAS  PubMed  Google Scholar 

Xu J, Huang G, Zhang Z, Zhao J, Zhang M, Wang Y, et al. Up-Regulation of Glioma-Associated Oncogene Homolog 1 Expression by Serum Starvation Promotes Cell Survival in ER-Positive Breast Cancer Cells. Cell Physiol Biochem. 2015;36:1862–76.

Article  CAS  PubMed  Google Scholar 

Jank P, Karn T, van Mackelenbergh M, Lindner J, Treue D, Huober J, et al. An Analysis of Hotspot Mutations and Response to Neoadjuvant Therapy in Patients with Breast Cancer from Four Prospective Clinical Trials. Clinical Cancer Res. 2024;30:3868–80.

Article  CAS  Google Scholar 

Platten M, Nollen EAA, Röhrig UF, Fallarino F, Opitz CA. Tryptophan metabolism as a common therapeutic target in cancer, neurodegeneration and beyond. Nat Rev Drug Discov. 2019;18:379–401.

Article  CAS  PubMed  Google Scholar 

Mohamed E, Kumar A, Zhang Y, Wang AS, Chen K, Lim Y, et al. PI3K/AKT/mTOR signaling pathway activity in IDH-mutant diffuse glioma and clinical implications. Neuro Oncol. 2022;24:1471–81.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Gan ST, Macalinao DG, Shahoei SH, Tian L, Jin X, Basnet H, et al. Distinct tumor architectures and microenvironments for the initiation of breast cancer metastasis in the brain. Cancer Cell. 2024;42.

Lo Gullo R, Daimiel I, Morris EA, Pinker K. Combining molecular and imaging metrics in cancer: radiogenomics. Insights Imaging. 2020;11:1.

Article  PubMed  PubMed Central  Google Scholar 

Newitt D, Hylton N, Team. obotI-SNaAT. Multi-center breast DCE-MRI data and segmentations from patients in the I-SPY 1/ACRIN 6657 trials. The Cancer Imaging Archive http://doiorg/107937/K9/TCIA2016HdHpgJLK. 2016.

Bakas S, Sako C, Akbari H, Bilello M, Sotiras A, Shukla G, et al. The University of Pennsylvania glioblastoma (UPenn-GBM) cohort: advanced MRI, clinical, genomics, & radiomics. Sci Data. 2022;9:453.

Article  PubMed  PubMed Central  Google Scholar 

Saha A, Harowicz MR, Grimm LJ, Kim CE, Ghate SV, Walsh R, et al. A machine learning approach to radiogenomics of breast cancer: a study of 922 subjects and 529 DCE-MRI features. Br J Cancer. 2018;119:508–16.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Hylton NM, Gatsonis CA, Rosen MA, Lehman CD, Newitt DC, Partridge SC, et al. Neoadjuvant Chemotherapy for Breast Cancer: Functional Tumor Volume by MR Imaging Predicts Recurrence-free Survival-Results from the ACRIN 6657/CALGB 150007 I-SPY 1 TRIAL. Radiology. 2016;279:44–55.

Article  PubMed  Google Scholar 

Rohlfing T, Zahr NM, Sullivan EV, Pfefferbaum A. The SRI24 multichannel atlas of normal adult human brain structure. Hum Brain Mapp. 2010;31:798–819.

Article  PubMed  Google Scholar 

Fan M, Cheng H, Zhang P, Gao X, Zhang J, Shao G, et al. DCE-MRI texture analysis with tumor subregion partitioning for predicting Ki-67 status of estrogen receptor-positive breast cancers. Journal Magn Reson imaging : JMRI. 2018;48:237–47.

Article  PubMed  Google Scholar 

Fan M, Zhang Y, Fu Z, Xu M, Wang S, Xie S, et al. A deep matrix completion method for imputing missing histological data in breast cancer by integrating DCE-MRI radiomics. Medical physics. 2021.

Fan M, Zhang P, Wang Y, Peng W, Wang S, Gao X, et al. Radiomic analysis of imaging heterogeneity in tumours and the surrounding parenchyma based on unsupervised decomposition of DCE-MRI for predicting molecular subtypes of breast cancer. European Radiol. 2019;29:4456–67.

Article  Google Scholar 

Kamnitsas K, Ledig C, Newcombe VFJ, Simpson JP, Kane AD, Menon DK, et al. Efficient multi-scale 3D CNN with fully connected CRF for accurate brain lesion segmentation. Medical image Anal. 2017;36:61–78.

Article  Google Scholar 

McKinley R, Meier R, Wiest R: Ensembles of Densely-Connected CNNs with Label-Uncertainty for Brain Tumor Segmentation. In: 2019; Cham: Springer International Publishing; 2019:456-65.

Isensee F, Jaeger PF, Kohl SAA, Petersen J, Maier-Hein KH. nnU-Net: a self-configuring method for deep learning-based biomedical image segmentation. Nat Methods. 2021;18:203–11.

Article  CAS  PubMed  Google Scholar 

Warfield SK, Zou KH, Wells WM. Simultaneous truth and performance level estimation (STAPLE): an algorithm for the validation of image segmentation. IEEE Trans Med imaging. 2004;23:903–21.

Article  PubMed  PubMed Central  Google Scholar 

van Griethuysen JJM, Fedorov A, Parmar C, Hosny A, Aucoin N, Narayan V, et al. Computational Radiomics System to Decode the Radiographic Phenotype. Cancer Res. 2017;77:e104–e107.

Article  PubMed  PubMed Central  Google Scholar 

Fan M, Yuan W, Zhao W, Xu M, Wang S, Gao X, et al. Joint Prediction of Breast Cancer Histological Grade and Ki-67 Expression Level Based on DCE-MRI and DWI Radiomics. IEEE J Biomed health Inform. 2020;24:1632–42.

Article  PubMed  Google Scholar 

Ronneberger O, Fischer P, Brox T. U-Net: Convolutional Networks for Biomedical Image Segmentation. 2015.

Lin TY, Goyal P, Girshick R, He K, Dollár P: Focal Loss for Dense Object Detection. In: 2017 IEEE International Conference on Computer Vision (ICCV): 22–29 Oct. 2017;2017:2999-3007.

He K, Zhang X, Ren S, Sun J: Deep Residual Learning for Image Recognition. In: 2016 IEEE Conference on Computer Vision and Pattern Recognition (CVPR): 27–30 June 2016 2016;2016:770-8.

Melekhov I, Kannala J, Rahtu E. Siamese network features for image matching. 2016 23rd Int Conf Pattern Recognit (ICPR). 2016;2016:378–83.

Article  Google Scholar 

Tang D, Zhao X, Zhang L, Wang Z, Wang C. Identification of hub genes to regulate breast cancer metastasis to brain by bioinformatics analyses. J Cell Biochem. 2019;120:9522–31.

Article  CAS  PubMed  Google Scholar 

Wehrle-Haller B. Structure and function of focal adhesions. Curr Opin Cell Biol. 2012;24:116–24.

Article  CAS  PubMed  Google Scholar 

Nersisyan S, Novosad V, Engibaryan N, Ushkaryov Y, Nikulin S, Tonevitsky A. ECM-Receptor Regulatory Network and Its Prognostic Role in Colorectal Cancer. Front Genet. 2021;12:782699.

Article  CAS  PubMed  PubMed Central  Google Scholar