The Cancer Genome Atlas cohort

Aliases

TCGA

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Mentioned in (67)

Papers in which this entity is mentioned.

• Extrachromosomal DNA-Driven Oncogene Spatial Heterogeneity and Evolution in Glioblastoma. (2025)
• Tumour-wide RNA splicing aberrations generate actionable public neoantigens. (2025)
• Chromosomal instability as a driver of cancer progression. (2025)
• Efficient and accurate search in petabase-scale sequence repositories. (2025)
• Flexynesis: A deep learning toolkit for bulk multi-omics data integration for precision oncology and beyond. (2025)
• Foundation models in bioinformatics. (2025)
• Splicing neoantigen discovery with SNAF reveals shared targets for cancer immunotherapy. (2024)
• Insights for precision oncology from the integration of genomic and clinical data of 13,880 tumors from the 100,000 Genomes Cancer Programme. (2024)
• A New Era of Data-Driven Cancer Research and Care: Opportunities and Challenges. (2024)
• Combination of genomic instability score and TP53 status for prognosis prediction in lung adenocarcinoma. (2023)
• A DNA methylation atlas of normal human cell types. (2023)
• Immune selection determines tumor antigenicity and influences response to checkpoint inhibitors. (2023)
• Spatially resolved whole transcriptome profiling in human and mouse tissue using Digital Spatial Profiling. (2022)
• Inferring gene expression from cell-free DNA fragmentation profiles. (2022)
• Integrating molecular profiles into clinical frameworks through the Molecular Oncology Almanac to prospectively guide precision oncology. (2021)
• Application of third-generation sequencing in cancer research. (2021)
• Evaluating the transcriptional fidelity of cancer models. (2021)
• Integrative reconstruction of cancer genome karyotypes using InfoGenomeR. (2021)
• Characterizing genetic intra-tumor heterogeneity across 2,658 human cancer genomes. (2021)
• Best practices for variant calling in clinical sequencing. (2020)
• Extrachromosomal DNA is associated with oncogene amplification and poor outcome across multiple cancers. (2020)
• Establishing guidelines to harmonize tumor mutational burden (TMB): in silico assessment of variation in TMB quantification across diagnostic platforms: phase I of the Friends of Cancer Research TMB Harmonization Project. (2020)
• CHASMplus Reveals the Scope of Somatic Missense Mutations Driving Human Cancers. (2019)
• Passenger hotspot mutations in cancer driven by APOBEC3A and mesoscale genomic features. (2019)
• The mutational constraint spectrum quantified from variation in 141,456 humans (2019)
• Tumor mutational burden standardization initiatives: Recommendations for consistent tumor mutational burden assessment in clinical samples to guide immunotherapy treatment decisions. (2019)
• Association of BRCA1- and BRCA2-deficiency with mutation burden, expression of PD-L1/PD-1, immune infiltrates, and T cell-inflamed signature in breast cancer. (2019)
• Best practices for bioinformatic characterization of neoantigens for clinical utility. (2019)
• Identifying simultaneous rearrangements in cancer genomes. (2018)
• Driver Fusions and Their Implications in the Development and Treatment of Human Cancers. (2018)
• Comprehensive Characterization of Cancer Driver Genes and Mutations. (2018)
• Genome doubling shapes the evolution and prognosis of advanced cancers. (2018)
• The Immune Landscape of Cancer. (2018)
• Characterizing genetic intra-tumor heterogeneity across 2,658 human cancer genomes (2018)
• Predicting T cell recognition of MHC class I restricted neoepitopes. (2018)
• Patterns and mechanisms of structural variations in human cancer. (2018)
• OncoKB: A Precision Oncology Knowledge Base. (2017)
• Integrative clustering of multi-level 'omic data based on non-negative matrix factorization algorithm. (2017)
• Integrated analysis of gene expression and copy number identified potential cancer driver genes with amplification-dependent overexpression in 1,454 solid tumors. (2017)
• CScape: a tool for predicting oncogenic single-point mutations in the cancer genome. (2017)
• Recurrent mutation of IGF signalling genes and distinct patterns of genomic rearrangement in osteosarcoma. (2017)
• Tumor phylogeny inference using tree-constrained importance sampling. (2017)
• Comprehensive Analysis of Hypermutation in Human Cancer. (2017)
• The real cost of sequencing: scaling computation to keep pace with data generation. (2016)
• B lymphocytes and cancer: a love-hate relationship. (2016)
• Exploring genomic alteration in pediatric cancer using ProteinPaint. (2016)
• Association of germline variants in the APOBEC3 region with cancer risk and enrichment with APOBEC-signature mutations in tumors. (2016)
• Somatic cancer variant curation and harmonization through consensus minimum variant level data. (2016)
• DeconstructSigs: delineating mutational processes in single tumors distinguishes DNA repair deficiencies and patterns of carcinoma evolution. (2016)
• Global analysis of somatic structural genomic alterations and their impact on gene expression in diverse human cancers. (2016)
• FACETS: allele-specific copy number and clonal heterogeneity analysis tool for high-throughput DNA sequencing. (2016)
• Comprehensive analyses of tumor immunity: implications for cancer immunotherapy. (2016)
• GenVisR: Genomic Visualizations in R. (2016)
• DGIdb 2.0: mining clinically relevant drug-gene interactions. (2016)
• Estimating the population abundance of tissue-infiltrating immune and stromal cell populations using gene expression. (2016)
• Clock-like mutational processes in human somatic cells. (2015)
• Profiling tissue-resident T cell repertoires by RNA sequencing. (2015)
• The landscape of long noncoding RNAs in the human transcriptome. (2015)
• Reconstructing A/B compartments as revealed by Hi-C using long-range correlations in epigenetic data. (2015)
• Genome-wide analysis of noncoding regulatory mutations in cancer. (2014)
• THetA: inferring intra-tumor heterogeneity from high-throughput DNA sequencing data. (2013)
• Signatures of mutational processes in human cancer. (2013)
• Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples. (2013)
• Assessing telomeric DNA content in pediatric cancers using whole-genome sequencing data. (2012)
• A framework for variation discovery and genotyping using next-generation DNA sequencing data. (2011)
• The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. (2010)
• Tackling the widespread and critical impact of batch effects in high-throughput data. (2010)

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