tumor phenotype

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Mentioned in (132)

Papers in which this entity is mentioned.

• A guide to transcriptomic deconvolution in cancer. (2026)
• Investigation of a global mouse methylome atlas reveals subtype-specific copy number alterations in pediatric cancer models. (2026)
• Stratified Medicine Pediatrics: Cell-Free DNA and Serial Tumor Sequencing Identifies Subtype-Specific Cancer Evolution and Epigenetic States. (2025)
• Extrachromosomal DNA-Driven Oncogene Spatial Heterogeneity and Evolution in Glioblastoma. (2025)
• Rapid brain tumor classification from sparse epigenomic data. (2025)
• Three-dimensional genome landscape of primary human cancers. (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)
• Tumor-informed deep sequencing of ctDNA detects minimal residual disease and predicts relapse in osteosarcoma. (2024)
• The landscape of drug sensitivity and resistance in sarcoma. (2024)
• Analysis of 10,478 cancer genomes identifies candidate driver genes and opportunities for precision oncology. (2024)
• ENPP1 Immunobiology as a Therapeutic Target. (2023)
• Comprehensive analysis of mutational signatures reveals distinct patterns and molecular processes across 27 pediatric cancers. (2023)
• Immune selection determines tumor antigenicity and influences response to checkpoint inhibitors. (2023)
• Single-molecule methylation profiles of cell-free DNA in cancer with nanopore sequencing. (2023)
• RNA splicing dysregulation and the hallmarks of cancer. (2023)
• Nucleosome footprinting in plasma cell-free DNA for the pre-surgical diagnosis of ovarian cancer. (2022)
• At the dawn: cell-free DNA fragmentomics and gene regulation. (2022)
• Genome-wide mutational signatures in low-coverage whole genome sequencing of cell-free DNA. (2022)
• Single-cell analysis of hepatoblastoma identifies tumor signatures that predict chemotherapy susceptibility using patient-specific tumor spheroids. (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)
• Feasibility of whole genome and transcriptome profiling in pediatric and young adult cancers. (2022)
• Circulating Tumor DNA as a Biomarker in Patients With Stage III and IV Wilms Tumor: Analysis From a Children's Oncology Group Trial, AREN0533. (2022)
• Enhanced detection of minimal residual disease by targeted sequencing of phased variants in circulating tumor DNA. (2021)
• Integrated Genomic Analysis Identifies Driver Genes and Cisplatin-Resistant Progenitor Phenotype in Pediatric Liver Cancer. (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)
• A practical guide to cancer subclonal reconstruction from DNA sequencing. (2021)
• A Comprehensive Circulating Tumor DNA Assay for Detection of Translocation and Copy-Number Changes in Pediatric Sarcomas. (2021)
• SPOTlight: seeded NMF regression to deconvolute spatial transcriptomics spots with single-cell transcriptomes. (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)
• MHCAttnNet: predicting MHC-peptide bindings for MHC alleles classes I and II using an attention-based deep neural model. (2020)
• DNA mismatch repair promotes APOBEC3-mediated diffuse hypermutation in human cancers. (2020)
• Immuno-genomic landscape of osteosarcoma. (2020)
• Genome-wide cell-free DNA mutational integration enables ultra-sensitive cancer monitoring. (2020)
• Ewing sarcoma with FEV gene rearrangements is a rare subset with predilection for extraskeletal locations and aggressive behavior. (2020)
• Accucopy: Accurate and Fast Inference of Allele-specific Copy Number Alterations from Low-coverage Low-purity Tumor Sequencing Data (2020)
• Neoadjuvant checkpoint blockade for cancer immunotherapy. (2020)
• Comprehensive analysis of structural variants in breast cancer genomes using single-molecule sequencing. (2020)
• Ploidy- and Purity-Adjusted Allele-Specific DNA Analysis Using CLONETv2. (2019)
• Exploring the landscape of focal amplifications in cancer using AmpliconArchitect. (2019)
• The mutational footprints of cancer therapies. (2019)
• Determining cell type abundance and expression from bulk tissues with digital cytometry. (2019)
• Rare variant phasing using paired tumor:normal sequence data. (2019)
• Whole-exome sequencing of cervical carcinomas identifies activating ERBB2 and PIK3CA mutations as targets for combination therapy. (2019)
• Rapid and reversible suppression of ALT by DAXX in osteosarcoma cells. (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)
• Best practices for bioinformatic characterization of neoantigens for clinical utility. (2019)
• Comprehensive analysis of structural variants in breast cancer genomes using single molecule sequencing (2019)
• CALDER: Inferring Phylogenetic Trees from Longitudinal Tumor Samples. (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)
• Driver Fusions and Their Implications in the Development and Treatment of Human Cancers. (2018)
• GeneGini: Assessment via the Gini Coefficient of Reference "Housekeeping" Genes and Diverse Human Transporter Expression Profiles. (2018)
• Widespread Selection for Oncogenic Mutant Allele Imbalance in Cancer. (2018)
• Genome-wide somatic variant calling using localized colored de Bruijn graphs. (2018)
• Positively selected enhancer elements endow osteosarcoma cells with metastatic competence. (2018)
• The Immune Landscape of Cancer. (2018)
• Comprehensive Cancer-Predisposition Gene Testing in an Adult Multiple Primary Tumor Series Shows a Broad Range of Deleterious Variants and Atypical Tumor Phenotypes. (2018)
• Clinical cancer genomic profiling by three-platform sequencing of whole genome, whole exome and transcriptome. (2018)
• SvABA: genome-wide detection of structural variants and indels by local assembly. (2018)
• Universal Patterns of Selection in Cancer and Somatic Tissues. (2017)
• Integrated Molecular Meta-Analysis of 1,000 Pediatric High-Grade and Diffuse Intrinsic Pontine Glioma. (2017)
• ChimeRScope: a novel alignment-free algorithm for fusion transcript prediction using paired-end RNA-Seq data. (2017)
• XBSeq2: a fast and accurate quantification of differential expression and differential polyadenylation. (2017)
• Patient-derived xenografts undergo mouse-specific tumor evolution. (2017)
• Integrated analysis of gene expression and copy number identified potential cancer driver genes with amplification-dependent overexpression in 1,454 solid tumors. (2017)
• Orthotopic patient-derived xenografts of paediatric solid tumours. (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)
• Scalable whole-exome sequencing of cell-free DNA reveals high concordance with metastatic tumors. (2017)
• A method to reduce ancestry related germline false positives in tumor only somatic variant calling. (2017)
• Tumor phylogeny inference using tree-constrained importance sampling. (2017)
• PGBD5 promotes site-specific oncogenic mutations in human tumors. (2017)
• Comprehensive Analysis of Hypermutation in Human Cancer. (2017)
• B lymphocytes and cancer: a love-hate relationship. (2016)
• Visualizing tumor evolution with the fishplot package for R. (2016)
• Global analysis of somatic structural genomic alterations and their impact on gene expression in diverse human cancers. (2016)
• ascatNgs: Identifying Somatically Acquired Copy-Number Alterations from Whole-Genome Sequencing Data. (2016)
• Landscape of somatic mutations in 560 breast cancer whole-genome sequences. (2016)
• Divergent clonal evolution of castration-resistant neuroendocrine prostate cancer. (2016)
• A genomic case study of desmoplastic small round cell tumor: comprehensive analysis reveals insights into potential therapeutic targets and development of a monitoring tool for a rare and aggressive disease. (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)
• 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)
• ENVE: a novel computational framework characterizes copy-number mutational landscapes in colorectal cancers from African American patients. (2015)
• Spatial reconstruction of single-cell gene expression data. (2015)
• Profiling tissue-resident T cell repertoires by RNA sequencing. (2015)
• Robust enumeration of cell subsets from tissue expression profiles. (2015)
• MBASED: allele-specific expression detection in cancer tissues and cell lines. (2014)
• Unraveling the clonal hierarchy of somatic genomic aberrations. (2014)
• CDK9-mediated transcription elongation is required for MYC addiction in hepatocellular carcinoma. (2014)
• Whole-exome sequencing and clinical interpretation of formalin-fixed, paraffin-embedded tumor samples to guide precision cancer medicine. (2014)
• Dynamic analyses of alternative polyadenylation from RNA-seq reveal a 3'-UTR landscape across seven tumour types. (2014)
• Involvement of p53 in the repair of DNA double strand breaks: multifaceted Roles of p53 in homologous recombination repair (HRR) and non-homologous end joining (NHEJ). (2014)
• Clonal evolution in hematological malignancies and therapeutic implications. (2014)
• TITAN: inference of copy number architectures in clonal cell populations from tumor whole-genome sequence data. (2014)
• PyClone: statistical inference of clonal population structure in cancer. (2014)
• Cancer genome landscapes. (2013)
• THetA: inferring intra-tumor heterogeneity from high-throughput DNA sequencing data. (2013)
• A simple consensus approach improves somatic mutation prediction accuracy. (2013)
• Integrative analysis of complex cancer genomics and clinical profiles using the cBioPortal. (2013)
• ACMG clinical laboratory standards for next-generation sequencing. (2013)
• A rare population of CD24(+)ITGB4(+)Notch(hi) cells drives tumor propagation in NSCLC and requires Notch3 for self-renewal. (2013)
• Mutational heterogeneity in cancer and the search for new cancer-associated genes. (2013)
• Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples. (2013)
• LIN28B promotes growth and tumorigenesis of the intestinal epithelium via Let-7. (2013)
• Clustered mutations in yeast and in human cancers can arise from damaged long single-strand DNA regions. (2012)
• Myeloid cells in tumor inflammation. (2012)
• Mutational processes molding the genomes of 21 breast cancers. (2012)
• Assessing telomeric DNA content in pediatric cancers using whole-genome sequencing data. (2012)
• VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing. (2012)
• Summarizing and correcting the GC content bias in high-throughput sequencing. (2012)
• HLA typing from RNA-Seq sequence reads. (2012)
• Massive genomic rearrangement acquired in a single catastrophic event during cancer development. (2011)
• Copy number variation detection in whole-genome sequencing data using the Bayesian information criterion. (2011)
• Allele-specific copy number analysis of tumors. (2010)
• Integrative analysis of the melanoma transcriptome. (2010)
• rSW-seq: algorithm for detection of copy number alterations in deep sequencing data. (2010)
• TumorBoost: normalization of allele-specific tumor copy numbers from a single pair of tumor-normal genotyping microarrays. (2010)
• BreakDancer: an algorithm for high-resolution mapping of genomic structural variation. (2009)
• Recurring mutations found by sequencing an acute myeloid leukemia genome. (2009)
• High-resolution mapping of copy-number alterations with massively parallel sequencing. (2009)
• Cancer-specific high-throughput annotation of somatic mutations: computational prediction of driver missense mutations. (2009)

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