Inferring spatial transcriptomics markers from whole slide images to characterize metastasis-related spatial heterogeneity of colorectal tumors: A pilot study
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Joshua J. Levy | Scott M. Palisoul | B. Christensen | Zarif L. Azher | L. Vaickus | L. Salas | G. Tsongalis | Rachael E. Barney | Eric Feng | F. Kolling | Cyril Sharma | Michael Fatemi | Tarushii Goel | O. Ramwala | Lucas A. Salas | Laurent Perreard | Laurent Perreard | Michael Fatemi | Eric Feng | Cyril Sharma | Zarif Azher | Tarushii Goel | Ojas Ramwala | Scott Palisoul | Rachael Barney | Fred Kolling | Brock C. Christensen | Gregory Tsongalis | Louis Vaickus | Joshua J. Levy | Michael Y Fatemi | Fred W. Kolling | Ojas Ramwala
[1] Xinhan Zhao,et al. A pan-cancer analysis of collagen VI family on prognosis, tumor microenvironment, and its potential therapeutic effect , 2022, BMC Bioinformatics.
[2] A. Suwalska,et al. Quantifying Spatial Heterogeneity of Tumor-Infiltrating Lymphocytes to Predict Survival of Individual Cancer Patients , 2022, Journal of personalized medicine.
[3] Clive Da Costa,et al. Gremlin-1 Promotes Colorectal Cancer Cell Metastasis by Activating ATF6 and Inhibiting ATF4 Pathways , 2022, Cells.
[4] Yuedong Yang,et al. Spatial Transcriptomics Prediction from Histology jointly through Transformer and Graph Neural Networks , 2022, bioRxiv.
[5] R. Geiger,et al. Identification of TPM2 and CNN1 as Novel Prognostic Markers in Functionally Characterized Human Colon Cancer-Associated Stromal Cells , 2022, Cancers.
[6] P. Laurent-Puig,et al. Tertiary lymphoid structures generate and propagate anti-tumor antibody-producing plasma cells in renal cell cancer. , 2022, Immunity.
[7] Tianhua Zhou,et al. Cadherin 11-mediated juxtacrine interaction of gastric cancer cells and fibroblasts promotes metastasis via YAP/tenascin-C signaling. , 2022, Science bulletin.
[8] Q. Gao,et al. Spatial omics: Navigating to the golden era of cancer research , 2022, Clinical and translational medicine.
[9] Di Zhang,et al. Proteomics and liquid biopsy characterization of human EMT-related metastasis in colorectal cancer , 2021, Frontiers in Oncology.
[10] L. Pachter,et al. Museum of spatial transcriptomics , 2020, Nature Methods.
[11] Guangming Li,et al. Identification of Ferroptosis-Related Genes Signature Predicting the Efficiency of Invasion and Metastasis Ability in Colon Adenocarcinoma , 2022, Frontiers in Cell and Developmental Biology.
[12] Q. Ji,et al. Resistance to anti-EGFR therapies in metastatic colorectal cancer: underlying mechanisms and reversal strategies , 2021, Journal of experimental & clinical cancer research : CR.
[13] Joshua J. Levy,et al. Mixed Effects Machine Learning Models for Colon Cancer Metastasis Prediction using Spatially Localized Immuno-Oncology Markers , 2021, bioRxiv.
[14] Xiangwei Meng,et al. SERPINE1 associated with remodeling of the tumor microenvironment in colon cancer progression: a novel therapeutic target , 2021, BMC cancer.
[15] Xiang Zhou,et al. SPARK-X: non-parametric modeling enables scalable and robust detection of spatial expression patterns for large spatial transcriptomic studies , 2021, Genome Biology.
[16] Hang Zheng,et al. Weighted Gene Co-expression Network Analysis Identifies CALD1 as a Biomarker Related to M2 Macrophages Infiltration in Stage III and IV Mismatch Repair-Proficient Colorectal Carcinoma , 2021, Frontiers in Molecular Biosciences.
[17] D. Schrag,et al. Diagnosis and Treatment of Metastatic Colorectal Cancer: A Review. , 2021, JAMA.
[18] Lia S. Campos,et al. Mapping the temporal and spatial dynamics of the human endometrium in vivo and in vitro , 2021, Nature Genetics.
[19] N. Ashley,et al. Spatiotemporal analysis of human intestinal development at single-cell resolution , 2021, Cell.
[20] V. Marx. Method of the Year: spatially resolved transcriptomics , 2021, Nature Methods.
[21] Alberto Dassatti,et al. giotto-tda: A Topological Data Analysis Toolkit for Machine Learning and Data Exploration , 2020, J. Mach. Learn. Res..
[22] J. Kleinman,et al. Transcriptome-scale spatial gene expression in the human dorsolateral prefrontal cortex , 2020, Nature Neuroscience.
[23] David F. Boyd,et al. Exuberant fibroblast activity compromises lung function via ADAMTS4 , 2020, Nature.
[24] J. Galon,et al. The immune contexture and Immunoscore in cancer prognosis and therapeutic efficacy , 2020, Nature Reviews Cancer.
[25] Z. Yakhini,et al. Spatial transcriptomics inferred from pathology whole-slide images links tumor heterogeneity to survival in breast and lung cancer , 2020, Scientific Reports.
[26] James Y. Zou,et al. Integrating spatial gene expression and breast tumour morphology via deep learning , 2020, Nature Biomedical Engineering.
[27] Adam J. Rubin,et al. Multimodal Analysis of Composition and Spatial Architecture in Human Squamous Cell Carcinoma , 2020, Cell.
[28] H. Ueno,et al. Spatial immune profiling of the colorectal tumor microenvironment predicts good outcome in stage II patients , 2020, npj Digital Medicine.
[29] A. Benson,et al. Contribution of Immunoscore and Molecular Features to Survival Prediction in Stage III Colon Cancer , 2020, JNCI cancer spectrum.
[30] Zhi‐Jie Zheng,et al. Differences in Incidence and Mortality Trends of Colorectal Cancer, Worldwide, Based on Sex, Age, and Anatomic Location. , 2020, Clinical gastroenterology and hepatology : the official clinical practice journal of the American Gastroenterological Association.
[31] B. Xing,et al. THBS1 facilitates colorectal liver metastasis through enhancing epithelial–mesenchymal transition , 2020, Clinical and Translational Oncology.
[32] T. Low,et al. Revisiting the Roles of Pro-Metastatic EpCAM in Cancer , 2020, Biomolecules.
[33] Wenjun Chang,et al. High stromal nicotinamide N‐methyltransferase (NNMT) indicates poor prognosis in colorectal cancer , 2020, Cancer medicine.
[34] Christopher J. Sevinsky,et al. Spatial domain analysis predicts risk of colorectal cancer recurrence and infers associated tumor microenvironment networks , 2020, Nature Communications.
[35] David Eargle,et al. Kepler Mapper: A flexible Python implementation of the Mapper algorithm , 2019, J. Open Source Softw..
[36] X. Fang,et al. O-GlcNAcylation of ITGA5 facilitates the occurrence and development of colorectal cancer. , 2019, Experimental cell research.
[37] J. Hadfield,et al. RNA sequencing: the teenage years , 2019, Nature Reviews Genetics.
[38] Baojun Wang,et al. PABPC1L depletion inhibits proliferation and migration via blockage of AKT pathway in human colorectal cancer cells , 2019, Oncology letters.
[39] A. Rao,et al. Spatial and phenotypic immune profiling of metastatic colon cancer. , 2018, JCI insight.
[40] T. Luider,et al. Up-regulation of collagen proteins in colorectal liver metastasis compared with normal liver tissue , 2018, The Journal of Biological Chemistry.
[41] M. Gerlinger,et al. Genomic and Transcriptomic Determinants of Therapy Resistance and Immune Landscape Evolution during Anti-EGFR Treatment in Colorectal Cancer , 2018, bioRxiv.
[42] I. Liu,et al. Extracellular domain of EpCAM enhances tumor progression through EGFR signaling in colon cancer cells. , 2018, Cancer letters.
[43] Leland McInnes,et al. UMAP: Uniform Manifold Approximation and Projection , 2018, J. Open Source Softw..
[44] Patrik L. Ståhl,et al. Spatial maps of prostate cancer transcriptomes reveal an unexplored landscape of heterogeneity , 2018, Nature Communications.
[45] Zhi-yan Hu,et al. FSTL1 interacts with VIM and promotes colorectal cancer metastasis via activating the focal adhesion signalling pathway , 2018, Cell Death & Disease.
[46] R. Weinberg,et al. Understanding the tumor immune microenvironment (TIME) for effective therapy , 2018, Nature Medicine.
[47] Xiao-Ming Wu,et al. Deeper Insights into Graph Convolutional Networks for Semi-Supervised Learning , 2018, AAAI.
[48] S. Teichmann,et al. SpatialDE: identification of spatially variable genes , 2018, Nature Methods.
[49] S. M. Hosseini,et al. VCAN gene expression and its association with tumor stage and lymph node metastasis in colorectal cancer patients , 2018 .
[50] T. Yoshikawa,et al. Clinical Significance of Tensin 4 Gene Expression in Patients with Gastric Cancer. , 2017, In vivo.
[51] B. Carneiro,et al. Wnt/beta-catenin pathway: modulating anticancer immune response , 2017, Journal of Hematology & Oncology.
[52] M. Mokhtari,et al. EPCAM Expression in Colon Adenocarcinoma and its Relationship with TNM Staging , 2017, Advanced biomedical research.
[53] Leland McInnes,et al. hdbscan: Hierarchical density based clustering , 2017, J. Open Source Softw..
[54] R. Goldschmeding,et al. A potential role for CCN2/CTGF in aggressive colorectal cancer , 2016, Journal of Cell Communication and Signaling.
[55] A. Matheu,et al. SOX9-regulated cell plasticity in colorectal metastasis is attenuated by rapamycin , 2016, Scientific Reports.
[56] P. Lian,et al. Gas1 Inhibits Metastatic and Metabolic Phenotypes in Colorectal Carcinoma , 2016, Molecular Cancer Research.
[57] Patrik L. Ståhl,et al. Visualization and analysis of gene expression in tissue sections by spatial transcriptomics , 2016, Science.
[58] Reiko Nishihara,et al. Loss of CDH1 (E-cadherin) expression is associated with infiltrative tumour growth and lymph node metastasis , 2016, British Journal of Cancer.
[59] Geoffrey E. Hinton,et al. Deep Learning , 2015, Nature.
[60] Xianjun Zhu,et al. [Role of CTHRC1 in proliferation, migration and invasion of human colorectal cancer cells]. , 2015, Nan fang yi ke da xue xue bao = Journal of Southern Medical University.
[61] Edward Y. Chen,et al. Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool , 2013, BMC Bioinformatics.
[62] L. Lapierre,et al. Rab25 regulates integrin expression in polarized colonic epithelial cells , 2013, Molecular biology of the cell.
[63] G. Mills,et al. Rab25 in cancer: a brief update. , 2012, Biochemical Society transactions.
[64] Wancai Yang,et al. Decorin-mediated inhibition of colorectal cancer growth and migration is associated with E-cadherin in vitro and in mice. , 2012, Carcinogenesis.
[65] M. Senthil,et al. Prediction of the adequacy of lymph node retrieval in colon cancer by hospital type. , 2010, Archives of surgery.
[66] Nigel C Bird,et al. The role of cell adhesion molecules in the progression of colorectal cancer and the development of liver metastasis. , 2009, Cellular signalling.
[67] Christian Pilarsky,et al. An expression module of WIPF1-coexpressed genes identifies patients with favorable prognosis in three tumor types , 2009, Journal of Molecular Medicine.
[68] M. Lai,et al. Analysis of SOX9 expression in colorectal cancer. , 2008, American journal of clinical pathology.
[69] D. Evans,et al. Germline E-cadherin gene (CDH1) mutations predispose to familial gastric cancer and colorectal cancer. , 1999, Human molecular genetics.