TCGA cohort

Aliases

The Cancer Genome Atlas

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Mentioned in (131)

Papers in which this entity is mentioned.

• A guide to transcriptomic deconvolution in cancer. (2026)
• DrBioRight 2.0: an LLM-powered bioinformatics chatbot for large-scale cancer functional proteomics analysis. (2025)
• Tumour-wide RNA splicing aberrations generate actionable public neoantigens. (2025)
• Efficient and accurate search in petabase-scale sequence repositories. (2025)
• Functional analysis of cancer-associated germline risk variants. (2025)
• Three-dimensional genome landscape of primary human cancers. (2025)
• Flexynesis: A deep learning toolkit for bulk multi-omics data integration for precision oncology and beyond. (2025)
• Tracing the evolution of single-cell 3D genomes in Kras-driven cancers. (2025)
• Splicing neoantigen discovery with SNAF reveals shared targets for cancer immunotherapy. (2024)
• Transient loss of Polycomb components induces an epigenetic cancer fate. (2024)
• Analysis of 10,478 cancer genomes identifies candidate driver genes and opportunities for precision oncology. (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)
• Deterministic evolution and stringent selection during preneoplasia. (2023)
• Immune selection determines tumor antigenicity and influences response to checkpoint inhibitors. (2023)
• Mapping clustered mutations in cancer reveals APOBEC3 mutagenesis of ecDNA. (2022)
• At the dawn: cell-free DNA fragmentomics and gene regulation. (2022)
• Estimation of tumor cell total mRNA expression in 15 cancer types predicts disease progression. (2022)
• Spatially resolved whole transcriptome profiling in human and mouse tissue using Digital Spatial Profiling. (2022)
• Detecting cell-of-origin and cancer-specific methylation features of cell-free DNA from Nanopore sequencing. (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)
• Accucopy: accurate and fast inference of allele-specific copy number alterations from low-coverage low-purity tumor sequencing data. (2021)
• Evaluating the transcriptional fidelity of cancer models. (2021)
• Integrative reconstruction of cancer genome karyotypes using InfoGenomeR. (2021)
• Detection and characterization of lung cancer using cell-free DNA fragmentomes. (2021)
• Data structures based on -mers for querying large collections of sequencing data sets. (2021)
• Biologically informed deep neural network for prostate cancer discovery. (2021)
• Characterizing genetic intra-tumor heterogeneity across 2,658 human cancer genomes. (2021)
• Pan-cancer analysis of longitudinal metastatic tumors reveals genomic alterations and immune landscape dynamics associated with pembrolizumab sensitivity. (2021)
• DNA mismatch repair promotes APOBEC3-mediated diffuse hypermutation in human cancers. (2020)
• B cells and tertiary lymphoid structures promote immunotherapy response. (2020)
• Immuno-genomic landscape of osteosarcoma. (2020)
• Genome-wide cell-free DNA mutational integration enables ultra-sensitive cancer monitoring. (2020)
• Pan-cancer analysis of whole genomes. (2020)
• Multi-cancer analysis of clonality and the timing of systemic spread in paired primary tumors and metastases. (2020)
• Inferring structural variant cancer cell fraction. (2020)
• The repertoire of mutational signatures in human cancer. (2020)
• Extrachromosomal DNA is associated with oncogene amplification and poor outcome across multiple cancers. (2020)
• Accucopy: Accurate and Fast Inference of Allele-specific Copy Number Alterations from Low-coverage Low-purity Tumor Sequencing Data (2020)
• Diverse noncoding mutations contribute to deregulation of cis-regulatory landscape in pediatric cancers. (2020)
• Comprehensive analysis of structural variants in breast cancer genomes using single-molecule sequencing. (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)
• Data structures based on <i>k</i> -mers for querying large collections of sequencing datasets (2019)
• Single-Cell RNA-Seq Reveals AML Hierarchies Relevant to Disease Progression and Immunity. (2019)
• CHASMplus Reveals the Scope of Somatic Missense Mutations Driving Human Cancers. (2019)
• Ploidy- and Purity-Adjusted Allele-Specific DNA Analysis Using CLONETv2. (2019)
• Exploring the landscape of focal amplifications in cancer using AmpliconArchitect. (2019)
• Passenger hotspot mutations in cancer driven by APOBEC3A and mesoscale genomic features. (2019)
• Determining cell type abundance and expression from bulk tissues with digital cytometry. (2019)
• Rare variant phasing using paired tumor:normal sequence data. (2019)
• Tumor mutational burden standardization initiatives: Recommendations for consistent tumor mutational burden assessment in clinical samples to guide immunotherapy treatment decisions. (2019)
• VCF2CNA: A tool for efficiently detecting copy-number alterations in VCF genotype data and tumor purity. (2019)
• Fast and robust deconvolution of tumor infiltrating lymphocyte from expression profiles using least trimmed squares. (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)
• Assessment of tumor mutation burden calculation from gene panel sequencing data. (2019)
• RNA sequence analysis reveals macroscopic somatic clonal expansion across normal tissues. (2019)
• CNVScope: Visually Exploring Copy Number Aberrations in Cancer Genomes. (2019)
• Single-cell multiomic analysis identifies regulatory programs in mixed-phenotype acute leukemia. (2019)
• Accurity: accurate tumor purity and ploidy inference from tumor-normal WGS data by jointly modelling somatic copy number alterations and heterozygous germline single-nucleotide-variants. (2018)
• mSignatureDB: a database for deciphering mutational signatures in human cancers. (2018)
• Driver Fusions and Their Implications in the Development and Treatment of Human Cancers. (2018)
• Pan-cancer genome and transcriptome analyses of 1,699 paediatric leukaemias and solid tumours. (2018)
• Quantification of subclonal selection in cancer from bulk sequencing data. (2018)
• Mutational processes shape the landscape of TP53 mutations in human cancer. (2018)
• Widespread Selection for Oncogenic Mutant Allele Imbalance in Cancer. (2018)
• Comprehensive Characterization of Cancer Driver Genes and Mutations. (2018)
• Genome-wide somatic variant calling using localized colored de Bruijn graphs. (2018)
• Genome doubling shapes the evolution and prognosis of advanced cancers. (2018)
• The Immune Landscape of Cancer. (2018)
• Robust prediction of response to immune checkpoint blockade therapy in metastatic melanoma. (2018)
• Profiling Tumor Infiltrating Immune Cells with CIBERSORT. (2018)
• Predicting T cell recognition of MHC class I restricted neoepitopes. (2018)
• SvABA: genome-wide detection of structural variants and indels by local assembly. (2018)
• Picky comprehensively detects high-resolution structural variants in nanopore long reads. (2018)
• Copy number signatures and mutational processes in ovarian carcinoma. (2018)
• Nanopore Sequencing Reveals High-Resolution Structural Variation in the Cancer Genome (2017)
• CRAVAT 4: Cancer-Related Analysis of Variants Toolkit. (2017)
• Analysis of 100,000 human cancer genomes reveals the landscape of tumor mutational burden. (2017)
• SVclone: inferring structural variant cancer cell fraction (2017)
• Universal Patterns of Selection in Cancer and Somatic Tissues. (2017)
• ChimeRScope: a novel alignment-free algorithm for fusion transcript prediction using paired-end RNA-Seq data. (2017)
• Integrative clustering of multi-level 'omic data based on non-negative matrix factorization algorithm. (2017)
• Patient-derived xenografts undergo mouse-specific tumor evolution. (2017)
• Allele-Specific HLA Loss and Immune Escape in Lung Cancer Evolution. (2017)
• Mutational landscape of metastatic cancer revealed from prospective clinical sequencing of 10,000 patients. (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)
• Copy-number signatures and mutational processes in ovarian carcinoma (2017)
• Toil enables reproducible, open source, big biomedical data analyses. (2017)
• Extrachromosomal oncogene amplification drives tumour evolution and genetic heterogeneity. (2017)
• An open access pilot freely sharing cancer genomic data from participants in Texas. (2016)
• B lymphocytes and cancer: a love-hate relationship. (2016)
• Association of germline variants in the APOBEC3 region with cancer risk and enrichment with APOBEC-signature mutations in tumors. (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)
• Divergent clonal evolution of castration-resistant neuroendocrine prostate cancer. (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)
• APOBEC-induced mutations in human cancers are strongly enriched on the lagging DNA strand during replication. (2016)
• Development and clinical application of an integrative genomic approach to personalized cancer therapy. (2016)
• Estimating the population abundance of tissue-infiltrating immune and stromal cell populations using gene expression. (2016)
• Quantifying Clonal and Subclonal Passenger Mutations in Cancer Evolution. (2016)
• Recurrent somatic mutations in regulatory regions of human cancer genomes. (2015)
• Sequenza: allele-specific copy number and mutation profiles from tumor sequencing data. (2015)
• Integrative clinical genomics of advanced prostate cancer. (2015)
• ENVE: a novel computational framework characterizes copy-number mutational landscapes in colorectal cancers from African American patients. (2015)
• Profiling tissue-resident T cell repertoires by RNA sequencing. (2015)
• Systematic pan-cancer analysis of tumour purity. (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)
• RADIA: RNA and DNA integrated analysis for somatic mutation detection. (2014)
• Genome-wide analysis of noncoding regulatory mutations in cancer. (2014)
• PVT1 dependence in cancer with MYC copy-number increase. (2014)
• Dynamic analyses of alternative polyadenylation from RNA-seq reveal a 3'-UTR landscape across seven tumour types. (2014)
• Normalization of RNA-seq data using factor analysis of control genes or samples. (2014)
• An ultrasensitive method for quantitating circulating tumor DNA with broad patient coverage. (2014)
• ABRA: improved coding indel detection via assembly-based realignment. (2014)
• The genomic landscape of the Ewing Sarcoma family of tumors reveals recurrent STAG2 mutation. (2014)
• Inferring tumour purity and stromal and immune cell admixture from expression data. (2013)
• Integrative analysis of complex cancer genomics and clinical profiles using the cBioPortal. (2013)
• Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. (2013)
• Emerging landscape of oncogenic signatures across human cancers. (2013)
• An APOBEC cytidine deaminase mutagenesis pattern is widespread in human cancers. (2013)
• Pan-cancer patterns of somatic copy number alteration. (2013)
• Absolute quantification of somatic DNA alterations in human cancer. (2012)
• VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing. (2012)
• GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers. (2011)
• Copy number variation detection in whole-genome sequencing data using the Bayesian information criterion. (2011)
• TumorBoost: normalization of allele-specific tumor copy numbers from a single pair of tumor-normal genotyping microarrays. (2010)

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