cancer phenotype

Aliases

any type of cancer, cancer, cancer risk, cancer-related networks, cancers, carcinogenesis, malignant neoplasms, multiple types of cancer, some types of cancer, tumor, various cancers

Related entities (4)

Mentioned in (346)

Papers in which this entity is mentioned.

• A guide to transcriptomic deconvolution in cancer. (2026)
• Comprehensive repertoire of the chromosomal alteration and mutational signatures across 16 cancer types. (2026)
• Investigation of a global mouse methylome atlas reveals subtype-specific copy number alterations in pediatric cancer models. (2026)
• Integrated in vivo combinatorial functional genomics and spatial transcriptomics of tumours to decode genotype-to-phenotype relationships. (2026)
• Single-cell exon deletion profiling reveals splicing events that shape gene expression and cell state dynamics. (2026)
• Whole-genome landscapes of 1,364 breast cancers. (2026)
• Whole genome sequencing approach to assess homologous recombination deficiency in a pan-cancer cohort. (2026)
• Annotating the genome at single-nucleotide resolution with DNA foundation models. (2025)
• Enhancer activation from transposable elements in extrachromosomal DNA. (2025)
• Nanopore-based cell-free DNA fragmentation and methylation profiles from the cerebral spinal fluid of patients with lung cancer brain metastases. (2025)
• Stratified Medicine Pediatrics: Cell-Free DNA and Serial Tumor Sequencing Identifies Subtype-Specific Cancer Evolution and Epigenetic States. (2025)
• Associations between common genetic variants and income provide insights about the socio-economic health gradient. (2025)
• DrBioRight 2.0: an LLM-powered bioinformatics chatbot for large-scale cancer functional proteomics analysis. (2025)
• Multigenerational cell tracking of DNA replication and heritable DNA damage. (2025)
• Rapid brain tumor classification from sparse epigenomic data. (2025)
• Chromosomal instability as a driver of cancer progression. (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)
• Single cell and spatial alternative splicing analysis with Nanopore long read sequencing. (2025)
• Alcohol Exposure May Increase Prenatal Choline Needs Through Redirection of Choline into Lipid Synthesis Rather than Methyl Donation. (2025)
• MYC ecDNA promotes intratumour heterogeneity and plasticity in PDAC. (2025)
• Transcription start sites experience a high influx of heritable variants fueled by early development. (2025)
• Parenting by individuals with fetal alcohol spectrum disorders and neurobehavioral outcomes in their offspring. (2024)
• Splicing neoantigen discovery with SNAF reveals shared targets for cancer immunotherapy. (2024)
• Integrative polygenic risk score improves the prediction accuracy of complex traits and diseases. (2024)
• Osteosarcoma PDX-Derived Cell Line Models for Preclinical Drug Evaluation Demonstrate Metastasis Inhibition by Dinaciclib through a Genome-Targeted Approach. (2024)
• Principles and methods for transferring polygenic risk scores across global populations. (2024)
• Detecting transposable elements in long-read genomes using sTELLeR. (2024)
• Machine-guided design of cell-type-targeting cis-regulatory elements. (2024)
• Molecular profiling of 888 pediatric tumors informs future precision trials and data-sharing initiatives in pediatric cancer. (2024)
• CAGI, the Critical Assessment of Genome Interpretation, establishes progress and prospects for computational genetic variant interpretation methods. (2024)
• Synthetic augmentation of cancer cell line multi-omic datasets using unsupervised deep learning. (2024)
• Transient loss of Polycomb components induces an epigenetic cancer fate. (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)
• Analysis of 10,478 cancer genomes identifies candidate driver genes and opportunities for precision oncology. (2024)
• The Application of Long-Read Sequencing to Cancer. (2024)
• A New Era of Data-Driven Cancer Research and Care: Opportunities and Challenges. (2024)
• MYC-Targeting Inhibitors Generated from a Stereodiversified Bicyclic Peptide Library. (2024)
• ENPP1 Immunobiology as a Therapeutic Target. (2023)
• A Novel Tissue-Free Method to Estimate Tumor-Derived Cell-Free DNA Quantity Using Tumor Methylation Patterns. (2023)
• Comprehensive repertoire of the chromosomal alteration and mutational signatures across 16 cancer types from 10,983 cancer patients (2023)
• Predicting tumour content of liquid biopsies from cell-free DNA. (2023)
• Adverse childhood experiences in children with fetal alcohol spectrum disorders and their effects on behavior. (2023)
• Heritable defects in telomere and mitotic function selectively predispose to sarcomas. (2023)
• Cell-Free DNA Fragmentomics: The Novel Promising Biomarker. (2023)
• ESPRESSO: Robust discovery and quantification of transcript isoforms from error-prone long-read RNA-seq data. (2023)
• A DNA methylation atlas of normal human cell types. (2023)
• Human 3D brain organoids: steering the demolecularization of brain and neurological diseases. (2023)
• Machine learning for genetics-based classification and treatment response prediction in cancer of unknown primary. (2023)
• Pitfalls of predicting age-related traits by polygenic risk scores. (2023)
• Deterministic evolution and stringent selection during preneoplasia. (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)
• Towards understandings of serine/arginine-rich splicing factors. (2023)
• Alternative splicing events as peripheral biomarkers for motor learning deficit caused by adverse prenatal environments. (2023)
• RNA splicing dysregulation and the hallmarks of cancer. (2023)
• Mapping clustered mutations in cancer reveals APOBEC3 mutagenesis of ecDNA. (2022)
• mutations, genetic mosaicism and human disease. (2022)
• 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)
• Single-cell analysis of somatic mutations in human bronchial epithelial cells in relation to aging and smoking. (2022)
• Genome-wide mutational signatures in low-coverage whole genome sequencing of cell-free DNA. (2022)
• Explainable multiview framework for dissecting spatial relationships from highly multiplexed data. (2022)
• Human Retrotransposons and Effective Computational Detection Methods for Next-Generation Sequencing Data. (2022)
• Variant interpretation using population databases: Lessons from gnomAD. (2022)
• Estimation of tumor cell total mRNA expression in 15 cancer types predicts disease progression. (2022)
• Cell-free DNA technologies for the analysis of brain cancer. (2022)
• The pro-apoptotic Bax gene modifies susceptibility to craniofacial dysmorphology following gastrulation-stage alcohol exposure. (2022)
• Single-cell genomic variation induced by mutational processes in cancer. (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)
• Construction and validation of a novel gene signature for predicting the prognosis of osteosarcoma. (2022)
• The GA4GH Phenopacket schema defines a computable representation of clinical data. (2022)
• Feasibility of whole genome and transcriptome profiling in pediatric and young adult cancers. (2022)
• Integrating molecular profiles into clinical frameworks through the Molecular Oncology Almanac to prospectively guide precision oncology. (2021)
• Enhanced detection of minimal residual disease by targeted sequencing of phased variants in circulating tumor DNA. (2021)
• Most non-canonical proteins uniquely populate the proteome or immunopeptidome. (2021)
• Prospective pan-cancer germline testing using MSK-IMPACT informs clinical translation in 751 patients with pediatric solid tumors. (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)
• Alternative splicing: Human disease and quantitative analysis from high-throughput sequencing. (2021)
• Detection of somatic structural variants from short-read next-generation sequencing data. (2021)
• Evaluating the transcriptional fidelity of cancer models. (2021)
• A practical guide to cancer subclonal reconstruction from DNA sequencing. (2021)
• Transcriptomic analyses of gastrulation-stage mouse embryos with differential susceptibility to alcohol. (2021)
• A Comprehensive Circulating Tumor DNA Assay for Detection of Translocation and Copy-Number Changes in Pediatric Sarcomas. (2021)
• Therapeutic Implications of Germline Testing in Patients With Advanced Cancers. (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)
• Accurate detection of circulating tumor DNA using nanopore consensus sequencing. (2021)
• Macrophage Polarization States in the Tumor Microenvironment. (2021)
• Prenatal alcohol exposure disrupts Sonic hedgehog pathway and primary cilia genes in the mouse neural tube. (2021)
• Characterizing genetic intra-tumor heterogeneity across 2,658 human cancer genomes. (2021)
• Simultaneous single cell measurements of intranuclear proteins and gene expression (2021)
• Best practices for variant calling in clinical sequencing. (2020)
• Structural variation in the sequencing era. (2020)
• DNA mismatch repair promotes APOBEC3-mediated diffuse hypermutation in human cancers. (2020)
• Immune network dysregulation associated with child neurodevelopmental delay: modulatory role of prenatal alcohol exposure. (2020)
• Genome-wide cell-free DNA mutational integration enables ultra-sensitive cancer monitoring. (2020)
• Pan-cancer analysis of whole genomes. (2020)
• Systematic evaluation of differential splicing tools for RNA-seq studies. (2020)
• Distinct Classes of Complex Structural Variation Uncovered across Thousands of Cancer Genome Graphs. (2020)
• Inferring structural variant cancer cell fraction. (2020)
• Emerging Roles of SRSF3 as a Therapeutic Target for Cancer. (2020)
• The repertoire of mutational signatures in human cancer. (2020)
• HSP70 and HSP90 in neurodegenerative diseases. (2020)
• Single-cell RNA landscape of intratumoral heterogeneity and immunosuppressive microenvironment in advanced osteosarcoma. (2020)
• ASEP: Gene-based detection of allele-specific expression across individuals in a population by RNA sequencing. (2020)
• Cancer PRSweb: An Online Repository with Polygenic Risk Scores for Major Cancer Traits and Their Evaluation in Two Independent Biobanks. (2020)
• Accucopy: Accurate and Fast Inference of Allele-specific Copy Number Alterations from Low-coverage Low-purity Tumor Sequencing Data (2020)
• The mutational constraint spectrum quantified from variation in 141,456 humans. (2020)
• Diverse noncoding mutations contribute to deregulation of cis-regulatory landscape in pediatric cancers. (2020)
• Neoadjuvant checkpoint blockade for cancer immunotherapy. (2020)
• Comprehensive germline genomic profiles of children, adolescents and young adults with solid tumors. (2020)
• Comprehensive analysis of structural variants in breast cancer genomes using single-molecule sequencing. (2020)
• Complete Response to PD-1 Inhibition in an Adolescent With Relapsed Clear Cell Adenocarcinoma of the Cervix Predicted by Neoepitope Burden and APOBEC Signature. (2020)
• Transcriptomic signatures across human tissues identify functional rare genetic variation. (2020)
• Data structures based on <i>k</i> -mers for querying large collections of sequencing datasets (2019)
• Liquid versus tissue biopsy for detecting acquired resistance and tumor heterogeneity in gastrointestinal cancers. (2019)
• Cannabinoids Exacerbate Alcohol Teratogenesis by a CB1-Hedgehog Interaction. (2019)
• CHASMplus Reveals the Scope of Somatic Missense Mutations Driving Human Cancers. (2019)
• Machine Learning-Enhanced T Cell Neoepitope Discovery for Immunotherapy Design. (2019)
• Super-enhancers: critical roles and therapeutic targets in hematologic malignancies. (2019)
• Exploring the landscape of focal amplifications in cancer using AmpliconArchitect. (2019)
• Comparative RNA-seq analysis aids in diagnosis of a rare pediatric tumor. (2019)
• HLA-VBSeq v2: improved HLA calling accuracy with full-length Japanese class-I panel. (2019)
• Passenger hotspot mutations in cancer driven by APOBEC3A and mesoscale genomic features. (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)
• The mutational constraint spectrum quantified from variation in 141,456 humans (2019)
• Whole-genome sequencing of triple-negative breast cancers in a population-based clinical study. (2019)
• A Pilot Follow-Up Study of Older Alcohol-Dependent COGA Adults. (2019)
• Designing combination therapies with modeling chaperoned machine learning. (2019)
• VCF2CNA: A tool for efficiently detecting copy-number alterations in VCF genotype data and tumor purity. (2019)
• Germline variants associated with leukocyte genes predict tumor recurrence in breast cancer patients. (2019)
• Structural variant calling: the long and the short of it. (2019)
• Genome-wide cell-free DNA fragmentation in patients with cancer. (2019)
• The role and robustness of the Gini coefficient as an unbiased tool for the selection of Gini genes for normalising expression profiling data. (2019)
• RNA sequence analysis reveals macroscopic somatic clonal expansion across normal tissues. (2019)
• A Compendium of Mutational Signatures of Environmental Agents. (2019)
• Comprehensive analysis of structural variants in breast cancer genomes using single molecule sequencing (2019)
• CNVScope: Visually Exploring Copy Number Aberrations in Cancer Genomes. (2019)
• Pan-cancer whole-genome analyses of metastatic solid tumours. (2019)
• CALDER: Inferring Phylogenetic Trees from Longitudinal Tumor Samples. (2019)
• Identifying simultaneous rearrangements in cancer genomes. (2018)
• Circular DNA elements of chromosomal origin are common in healthy human somatic tissue. (2018)
• 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)
• The Cancer Spliceome: Reprograming of Alternative Splicing in Cancer. (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)
• Rearrangement bursts generate canonical gene fusions in bone and soft tissue tumors. (2018)
• Enter the Matrix: Factorization Uncovers Knowledge from Omics. (2018)
• GeneGini: Assessment via the Gini Coefficient of Reference "Housekeeping" Genes and Diverse Human Transporter Expression Profiles. (2018)
• Detection of Somatic Structural Variants Enables Quantification and Characterization of Circulating Tumor DNA in Children With Solid Tumors. (2018)
• MutationalPatterns: comprehensive genome-wide analysis of mutational processes. (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)
• Enhanced detection of circulating tumor DNA by fragment size analysis. (2018)
• A compendium of conserved cleavage and polyadenylation events in mammalian genes. (2018)
• Positively selected enhancer elements endow osteosarcoma cells with metastatic competence. (2018)
• Complex rearrangements and oncogene amplifications revealed by long-read DNA and RNA sequencing of a breast cancer cell line. (2018)
• Personal Cancer Genome Reporter: variant interpretation report for precision oncology. (2018)
• The Immune Landscape of Cancer. (2018)
• PASSPORT-seq: A Novel High-Throughput Bioassay to Functionally Test Polymorphisms in Micro-RNA Target Sites. (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)
• Tumor fraction in cell-free DNA as a biomarker in prostate cancer. (2018)
• Characterizing genetic intra-tumor heterogeneity across 2,658 human cancer genomes (2018)
• A comparison of word embeddings for the biomedical natural language processing. (2018)
• Sensitivity to sequencing depth in single-cell cancer genomics. (2018)
• Predicting T cell recognition of MHC class I restricted neoepitopes. (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)
• Patterns and mechanisms of structural variations in human cancer. (2018)
• Picky comprehensively detects high-resolution structural variants in nanopore long reads. (2018)
• Thymic involution and rising disease incidence with age. (2018)
• Nanopore Sequencing Reveals High-Resolution Structural Variation in the Cancer Genome (2017)
• Analysis of 100,000 human cancer genomes reveals the landscape of tumor mutational burden. (2017)
• OncoKB: A Precision Oncology Knowledge Base. (2017)
• SVclone: inferring structural variant cancer cell fraction (2017)
• Fast and accurate HLA typing from short-read next-generation sequence data with xHLA. (2017)
• The evolution of tumour phylogenetics: principles and practice. (2017)
• Universal Patterns of Selection in Cancer and Somatic Tissues. (2017)
• Statistical algorithms improve accuracy of gene fusion detection. (2017)
• ChimeRScope: a novel alignment-free algorithm for fusion transcript prediction using paired-end RNA-Seq data. (2017)
• A pooled mutational analysis identifies ionizing radiation-associated mutational signatures conserved between mouse and human malignancies. (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)
• Integrated analysis of gene expression and copy number identified potential cancer driver genes with amplification-dependent overexpression in 1,454 solid tumors. (2017)
• The genomic landscape of balanced cytogenetic abnormalities associated with human congenital anomalies. (2017)
• Gene-environment interactions in development and disease. (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)
• Alternative Polyadenylation Directs Tissue-Specific miRNA Targeting in Somatic Tissues. (2017)
• Cancer-Specific Retargeting of BAF Complexes by a Prion-like Domain. (2017)
• A practical guide to single-cell RNA-sequencing for biomedical research and clinical applications. (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)
• ReMixT: clone-specific genomic structure estimation in cancer. (2017)
• Comprehensive Analysis of Hypermutation in Human Cancer. (2017)
• Extrachromosomal oncogene amplification drives tumour evolution and genetic heterogeneity. (2017)
• Clinical Assessment and Diagnosis of Germline Predisposition to Hematopoietic Malignancies: The University of Chicago Experience. (2017)
• Fast and Accurate Genomic Analyses using Genome Graphs (2017)
• An open access pilot freely sharing cancer genomic data from participants in Texas. (2016)
• The real cost of sequencing: scaling computation to keep pace with data generation. (2016)
• B lymphocytes and cancer: a love-hate relationship. (2016)
• Statistical modeling for sensitive detection of low-frequency single nucleotide variants. (2016)
• Visualizing tumor evolution with the fishplot package for R. (2016)
• New insights into the generation and role of de novo mutations in health and disease. (2016)
• A role for human homologous recombination factors in suppressing microhomology-mediated end joining. (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)
• Medulloblastoma-associated DDX3 variant selectively alters the translational response to stress. (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)
• The clinical trial landscape in oncology and connectivity of somatic mutational profiles to targeted therapies. (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)
• Evolutionary Insights into RNA trans-Splicing in Vertebrates. (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)
• 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)
• The Genetics of Fetal Alcohol Spectrum Disorders. (2016)
• Quantifying Clonal and Subclonal Passenger Mutations in Cancer Evolution. (2016)
• Genomic Characterization of Brain Metastases Reveals Branched Evolution and Potential Therapeutic Targets. (2015)
• The cell cycle regulator CCDC6 is a key target of RNA-binding protein EWS. (2015)
• EWS and FUS bind a subset of transcribed genes encoding proteins enriched in RNA regulatory functions. (2015)
• Recurrent somatic mutations in regulatory regions of human cancer genomes. (2015)
• Sequenza: allele-specific copy number and mutation profiles from tumor sequencing data. (2015)
• What Happens When Children with Fetal Alcohol Spectrum Disorders Become Adults? (2015)
• The human gene damage index as a gene-level approach to prioritizing exome variants. (2015)
• Candidate gene-environment interaction research: reflections and recommendations. (2015)
• Clock-like mutational processes in human somatic cells. (2015)
• Integrative Clinical Sequencing in the Management of Refractory or Relapsed Cancer in Youth. (2015)
• CONSERTING: integrating copy-number analysis with structural-variation detection. (2015)
• Experiences with workflows for automating data-intensive bioinformatics. (2015)
• HLAreporter: a tool for HLA typing from next generation sequencing data. (2015)
• Germline Mutations in Predisposition Genes in Pediatric Cancer. (2015)
• Systematic pan-cancer analysis of tumour purity. (2015)
• Comparison of RNA-seq and microarray-based models for clinical endpoint prediction. (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)
• Comprehensive genomic profiles of small cell lung cancer. (2015)
• Oncogenic fusion protein EWS-FLI1 is a network hub that regulates alternative splicing. (2015)
• A germline polymorphism of thymine DNA glycosylase induces genomic instability and cellular transformation. (2014)
• MBASED: allele-specific expression detection in cancer tissues and cell lines. (2014)
• Unraveling the clonal hierarchy of somatic genomic aberrations. (2014)
• Break-induced replication is a source of mutation clusters underlying kataegis. (2014)
• RADIA: RNA and DNA integrated analysis for somatic mutation detection. (2014)
• Genome-wide analysis of noncoding regulatory mutations in cancer. (2014)
• CDK9-mediated transcription elongation is required for MYC addiction in hepatocellular carcinoma. (2014)
• Maternal and neonatal plasma microRNA biomarkers for fetal alcohol exposure in an ovine model. (2014)
• Whole-exome sequencing and clinical interpretation of formalin-fixed, paraffin-embedded tumor samples to guide precision cancer medicine. (2014)
• Inference of high resolution HLA types using genome-wide RNA or DNA sequencing reads. (2014)
• Dynamic analyses of alternative polyadenylation from RNA-seq reveal a 3'-UTR landscape across seven tumour types. (2014)
• Recurrent somatic structural variations contribute to tumorigenesis in pediatric osteosarcoma. (2014)
• An ultrasensitive method for quantitating circulating tumor DNA with broad patient coverage. (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)
• Exon identity crisis: disease-causing mutations that disrupt the splicing code. (2014)
• EWS-FLI1 utilizes divergent chromatin remodeling mechanisms to directly activate or repress enhancer elements in Ewing sarcoma. (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)
• Prioritizing Potentially Druggable Mutations with dGene: An Annotation Tool for Cancer Genome Sequencing Data. (2013)
• Somatic rearrangements across cancer reveal classes of samples with distinct patterns of DNA breakage and rearrangement-induced hypermutability. (2013)
• Ewing sarcoma protein: a key player in human cancer. (2013)
• A simple consensus approach improves somatic mutation prediction accuracy. (2013)
• Integrative analysis of complex cancer genomics and clinical profiles using the cBioPortal. (2013)
• A meta-analysis of two genome-wide association studies to identify novel loci for maximum number of alcoholic drinks. (2013)
• Signatures of mutational processes in human cancer. (2013)
• Fusion genes and their discovery using high throughput sequencing. (2013)
• Mutational heterogeneity in cancer and the search for new cancer-associated genes. (2013)
• HLA typing from 1000 genomes whole genome and whole exome illumina data. (2013)
• Effects of alcohol on the endocrine system. (2013)
• Emerging landscape of oncogenic signatures across human cancers. (2013)
• A comparative analysis of algorithms for somatic SNV detection in cancer. (2013)
• DGIdb: mining the druggable genome. (2013)
• Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples. (2013)
• RNA splicing: a new player in the DNA damage response. (2013)
• An APOBEC cytidine deaminase mutagenesis pattern is widespread in human cancers. (2013)
• Reflections on the cost of "low-cost" whole genome sequencing: framing the health policy debate. (2013)
• Computational approaches to identify functional genetic variants in cancer genomes. (2013)
• Proteomic and bioinformatic analysis of mammalian SWI/SNF complexes identifies extensive roles in human malignancy. (2013)
• Pan-cancer patterns of somatic copy number alteration. (2013)
• LIN28B promotes growth and tumorigenesis of the intestinal epithelium via Let-7. (2013)
• Absolute quantification of somatic DNA alterations in human cancer. (2012)
• An Inv(16)(p13.3q24.3)-encoded CBFA2T3-GLIS2 fusion protein defines an aggressive subtype of pediatric acute megakaryoblastic leukemia. (2012)
• Improving bioinformatic pipelines for exome variant calling. (2012)
• Clustered mutations in yeast and in human cancers can arise from damaged long single-strand DNA regions. (2012)
• High-throughput detection of actionable genomic alterations in clinical tumor samples by targeted, massively parallel sequencing. (2012)
• Circular RNAs are the predominant transcript isoform from hundreds of human genes in diverse cell types. (2012)
• Molecular genetics of B-precursor acute lymphoblastic leukemia. (2012)
• Control-FREEC: a tool for assessing copy number and allelic content using next-generation sequencing data. (2012)
• Integrative analysis reveals relationships of genetic and epigenetic alterations in osteosarcoma. (2012)
• Mutational processes molding the genomes of 21 breast cancers. (2012)
• Novel mutations target distinct subgroups of medulloblastoma. (2012)
• AID/APOBEC cytosine deaminase induces genome-wide kataegis. (2012)
• Ultrasensitive detection of rare mutations using next-generation targeted resequencing. (2012)
• An integrated encyclopedia of DNA elements in the human genome. (2012)
• Assessing telomeric DNA content in pediatric cancers using whole-genome sequencing data. (2012)
• Detectable clonal mosaicism from birth to old age and its relationship to cancer. (2012)
• Genome sequencing of pediatric medulloblastoma links catastrophic DNA rearrangements with TP53 mutations. (2012)
• The Pediatric Cancer Genome Project. (2012)
• VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing. (2012)
• HLA typing from RNA-Seq sequence reads. (2012)
• GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers. (2011)
• A hidden Markov model for copy number variant prediction from whole genome resequencing data. (2011)
• Massive genomic rearrangement acquired in a single catastrophic event during cancer development. (2011)
• BRCA1 and BRCA2: different roles in a common pathway of genome protection. (2011)
• Outlier-Based Differential Expression Analysis in Proteomics Studies. (2011)
• A framework for variation discovery and genotyping using next-generation DNA sequencing data. (2011)
• Copy number variation detection in whole-genome sequencing data using the Bayesian information criterion. (2011)
• Mechanisms and consequences of alternative polyadenylation. (2011)
• Control-free calling of copy number alterations in deep-sequencing data using GC-content normalization. (2011)
• Allele-specific copy number analysis of tumors. (2010)
• Integrative analysis of the melanoma transcriptome. (2010)
• Comparison of Beta-value and M-value methods for quantifying methylation levels by microarray analysis. (2010)
• rSW-seq: algorithm for detection of copy number alterations in deep sequencing data. (2010)
• Nucleotide-resolution analysis of structural variants using BreakSeq and a breakpoint library. (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)
• Genomic copy number determination in cancer cells from single nucleotide polymorphism microarrays based on quantitative genotyping corrected for aneuploidy. (2009)
• Recurring mutations found by sequencing an acute myeloid leukemia genome. (2009)
• High-resolution mapping of copy-number alterations with massively parallel sequencing. (2009)
• Germline BRAF mutations in Noonan, LEOPARD, and cardiofaciocutaneous syndromes: molecular diversity and associated phenotypic spectrum. (2009)
• Copy-number-variation and copy-number-alteration region detection by cumulative plots. (2009)
• Cancer-specific high-throughput annotation of somatic mutations: computational prediction of driver missense mutations. (2009)
• 3' end mRNA processing: molecular mechanisms and implications for health and disease. (2008)
• RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays. (2008)
• Sequence variant classification and reporting: recommendations for improving the interpretation of cancer susceptibility genetic test results. (2008)
• MMEJ repair of double-strand breaks (director's cut): deleted sequences and alternative endings. (2008)
• MDM2 and MDM4: p53 regulators as targets in anticancer therapy. (2007)
• EWS, but not EWS-FLI-1, is associated with both TFIID and RNA polymerase II: interactions between two members of the TET family, EWS and hTAFII68, and subunits of TFIID and RNA polymerase II complexes. (1998)
• dNdScv
• GitHub - im3sanger/dndscv: dN/dS methods to quantify selection in cancer and somatic evolution · GitHub

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