National Cancer Institute's Genomic Data Commons
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National Cancer Institute's Genomic Data Commons
metasource: Fairsharing.org
version: FAIRsharing.org: NCI GDC; National Cancer Institute's Genomic Data Commons; DOI: https://doi.org/10.25504/FAIRsharing.RyVjoS; Last edited: July 31, 2020, 2:04 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
NCI GDC
metasource: Fairsharing.org
version: FAIRsharing.org: NCI GDC; National Cancer Institute's Genomic Data Commons; DOI: https://doi.org/10.25504/FAIRsharing.RyVjoS; Last edited: July 31, 2020, 2:04 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
Names
More detailed information about this field from each metasource.
National Cancer Institute's Genomic Data Commons
metasource: Fairsharing.orgversion: FAIRsharing.org: NCI GDC; National Cancer Institute's Genomic Data Commons; DOI: https://doi.org/10.25504/FAIRsharing.RyVjoS; Last edited: July 31, 2020, 2:04 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
NCI GDC
metasource: Fairsharing.orgversion: FAIRsharing.org: NCI GDC; National Cancer Institute's Genomic Data Commons; DOI: https://doi.org/10.25504/FAIRsharing.RyVjoS; Last edited: July 31, 2020, 2:04 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
Names
More detailed information about this field from each metasource.
National Cancer Institute's Genomic Data Commons
metasource: Fairsharing.orgversion: FAIRsharing.org: NCI GDC; National Cancer Institute's Genomic Data Commons; DOI: https://doi.org/10.25504/FAIRsharing.RyVjoS; Last edited: July 31, 2020, 2:04 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
NCI GDC
metasource: Fairsharing.orgversion: FAIRsharing.org: NCI GDC; National Cancer Institute's Genomic Data Commons; DOI: https://doi.org/10.25504/FAIRsharing.RyVjoS; Last edited: July 31, 2020, 2:04 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
The National Cancer Institute’s (NCI’s) Genomic Data Commons (GDC) is a data sharing The National Cancer Institute's Genomic Data Commons (GDC) was created to promote precision medicine in oncology. It supports the import and standardization of genomic and clinical data from cancer research programs. The GDC contains NCI-generated data from some of the largest and most comprehensive cancer genomic datasets, including The Cancer Genome Atlas (TCGA) and Therapeutically Applicable Research to Generate Effective Therapies (TARGET). For the first time, these datasets have been harmonized using a common set of bioinformatics pipelines, so that the data can be directly compared. As a growing knowledge system for cancer, the GDC also enables researchers to submit data, and harmonizes these data for import into the GDC.
Description
More detailed information about this field from each metasource.
The National Cancer Institute’s (NCI’s) Genomic Data Commons (GDC) is a data sharing The National Cancer Institute's Genomic Data Commons (GDC) was created to promote precision medicine in oncology. It supports the import and standardization of genomic and clinical data from cancer research programs. The GDC contains NCI-generated data from some of the largest and most comprehensive cancer genomic datasets, including The Cancer Genome Atlas (TCGA) and Therapeutically Applicable Research to Generate Effective Therapies (TARGET). For the first time, these datasets have been harmonized using a common set of bioinformatics pipelines, so that the data can be directly compared. As a growing knowledge system for cancer, the GDC also enables researchers to submit data, and harmonizes these data for import into the GDC.
metasource: Fairsharing.orgversion: FAIRsharing.org: NCI GDC; National Cancer Institute's Genomic Data Commons; DOI: https://doi.org/10.25504/FAIRsharing.RyVjoS; Last edited: July 31, 2020, 2:04 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
Webpage:
https://gdc.cancer.gov/Webpage
More detailed information about this field from each metasource.
https://gdc.cancer.gov/
metasource: Fairsharing.orgversion: FAIRsharing.org: NCI GDC; National Cancer Institute's Genomic Data Commons; DOI: https://doi.org/10.25504/FAIRsharing.RyVjoS; Last edited: July 31, 2020, 2:04 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
Publications:
Publications
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Toward a Shared Vision for Cancer Genomic Data
PMID: 27653561
metasource: Fairsharing.org
version: FAIRsharing.org: NCI GDC; National Cancer Institute's Genomic Data Commons; DOI: https://doi.org/10.25504/FAIRsharing.RyVjoS; Last edited: July 31, 2020, 2:04 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
Publications
More detailed information about this field from each metasource.
Toward a Shared Vision for Cancer Genomic Data
PMID: 27653561
metasource: Fairsharing.org
version: FAIRsharing.org: NCI GDC; National Cancer Institute's Genomic Data Commons; DOI: https://doi.org/10.25504/FAIRsharing.RyVjoS; Last edited: July 31, 2020, 2:04 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
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Toward a Shared Vision for Cancer Genomic Data
PubMed citations: 541.
541 articles citing: Toward a Shared Vision for Cancer Genomic Data
DNA methylation-based epigenetic signatures predict somatic genomic alterations in gliomas. PMID:35906213
Cancer-Associated Mutations of the Adenosine A2A Receptor Have Diverse Influences on Ligand Binding and Receptor Functions. PMID:35897852
A Regulatory Axis between Epithelial Splicing Regulatory Proteins and Estrogen Receptor α Modulates the Alternative Transcriptome of Luminal Breast Cancer. PMID:35887187
Structural Analysis of microRNAs in Myeloid Cancer Reveals Consensus Motifs. PMID:35885935
Discovering the drivers of clonal hematopoiesis. PMID:35871184
Targeting Mre11 overcomes platinum resistance and induces synthetic lethality in XRCC1 deficient epithelial ovarian cancers. PMID:35853939
Genome instability is associated with ethnic differences between Asians and Europeans in hepatocellular carcinoma. PMID:35832070
Integration of tumor extrinsic and intrinsic features associates with immunotherapy response in non-small cell lung cancer. PMID:35831288
N-myc Downstream-Regulated Gene 1 (NDRG1) Regulates Vascular Endothelial Growth Factor A (VEGFA) and Malignancies in Glioblastoma Multiforme (GBM). PMID:35813230
HunCRC: annotated pathological slides to enhance deep learning applications in colorectal cancer screening. PMID:35764660
Accurate Identification of Subclones in Tumor Genomes. PMID:35749590
Prediction of risk-associated genes and high-risk liver cancer patients from their mutation profile: benchmarking of mutation calling techniques. PMID:35734767
Contribution and clinical relevance of germline variation to the cancer transcriptome. PMID:35725412
An 8-Gene Signature for Classifying Major Subtypes of Non-Small-Cell Lung Cancer. PMID:35722224
Computational epigenetic landscape analysis reveals association of CACNA1G-AS1, F11-AS1, NNT-AS1, and MSC-AS1 lncRNAs in prostate cancer progression through aberrant methylation. PMID:35715447
Construction of a competing endogenous RNA network to analyse glucose-6-phosphate dehydrogenase dysregulation in hepatocellular carcinoma. PMID:35712981
Just Add Data: automated predictive modeling for knowledge discovery and feature selection. PMID:35710826
Genomic landscape of pathogenic mutation of APC, KRAS, TP53, PIK3CA, and MLH1 in Indonesian colorectal cancer. PMID:35709138
The DNA methylation landscape of five pediatric-tumor types. PMID:35707123
Signatures of copy number alterations in human cancer. PMID:35705804
Pan-cancer analysis of genomic scar patterns caused by homologous repair deficiency (HRD). PMID:35681079
Deep learning features encode interpretable morphologies within histological images. PMID:35676395
Structural bioinformatics enhances the interpretation of somatic mutations in KDM6A found in human cancers. PMID:35615018
In silico epitope prediction analyses highlight the potential for distracting antigen immunodominance with allogeneic cancer vaccines. PMID:35611186
Predicting cancer prognosis and drug response from the tumor microbiome. PMID:35610202
Construction of three-gene-based prognostic signature and analysis of immune cells infiltration in children and young adults with B-acute lymphoblastic leukemia. PMID:35603962
Human liver single nucleus and single cell RNA sequencing identify a hepatocellular carcinoma-associated cell-type affecting survival. PMID:35581624
Attribution of Cancer Origins to Endogenous, Exogenous, and Preventable Mutational Processes. PMID:35580068
Regulation of protein complex partners as a compensatory mechanism in aneuploid tumors. PMID:35575458
Consensus molecular subtype differences linking colon adenocarcinoma and obesity revealed by a cohort transcriptomic analysis. PMID:35560039
Curcumin and NCLX inhibitors share anti-tumoral mechanisms in microsatellite-instability-driven colorectal cancer. PMID:35526196
Detection of oncogenic and clinically actionable mutations in cancer genomes critically depends on variant calling tools. PMID:35512388
Deep neural network modeling identifies biomarkers of response to immune-checkpoint therapy. PMID:35494249
Identification of Stably Expressed Reference microRNAs in Epithelial Ovarian Cancer. PMID:35478140
Weight-bearing activity impairs nuclear membrane and genome integrity via YAP activation in plantar melanoma. PMID:35468978
Machine-Learning-Based Late Fusion on Multi-Omics and Multi-Scale Data for Non-Small-Cell Lung Cancer Diagnosis. PMID:35455716
Integrated bioinformatic pipeline using whole-exome and RNAseq data to identify germline variants correlated with cancer. PMID:35403010
RGMQL: scalable and interoperable computing of heterogeneous omics big data and metadata in R/Bioconductor. PMID:35392801
Homologous recombination deficiency is inversely correlated with microsatellite instability and identifies immunologically cold tumors in most cancer types. PMID:35384413
The genotypes and phenotypes of missense mutations in the proline domain of the p53 protein. PMID:35383292
Mechanistic Clues Provided by Concurrent Changes in the Expression of Genes Encoding the M1 Muscarinic Receptor, β-Catenin Signaling Proteins, and Downstream Targets in Adenocarcinomas of the Colon. PMID:35370785
Aneuploidy tolerance caused by BRG1 loss allows chromosome gains and recovery of fitness. PMID:35365638
Current progress and open challenges for applying deep learning across the biosciences. PMID:35365602
A single-cell analysis of breast cancer cell lines to study tumour heterogeneity and drug response. PMID:35361816
Solid Tumor Opioid Receptor Expression and Oncologic Outcomes: Analysis of the Cancer Genome Atlas and Genotype Tissue Expression Project. PMID:35359418
Anatomic position determines oncogenic specificity in melanoma. PMID:35355015
Specific human endogenous retroviruses predict metastatic potential in uveal melanoma. PMID:35349481
CRISPR activation screen identifies BCL-2 proteins and B3GNT2 as drivers of cancer resistance to T cell-mediated cytotoxicity. PMID:35338135
S100A4 Is a Strong Negative Prognostic Marker and Potential Therapeutic Target in Adenocarcinoma of the Stomach and Esophagus. PMID:35326507
Prognostic and biological role of the N-Myc downstream-regulated gene family in hepatocellular carcinoma. PMID:35321174
Nicotinamide (niacin) supplement increases lipid metabolism and ROS-induced energy disruption in triple-negative breast cancer: potential for drug repositioning as an anti-tumor agent. PMID:35278276
MITI minimum information guidelines for highly multiplexed tissue images. PMID:35277708
The Landscape of Actionable Genomic Alterations by Next-Generation Sequencing in Tumor Tissue Versus Circulating Tumor DNA in Chinese Patients With Non-Small Cell Lung Cancer. PMID:35273907
An integrative gene expression signature analysis identifies CMS4 KRAS-mutated colorectal cancers sensitive to combined MEK and SRC targeted therapy. PMID:35272617
Polo-like kinases as potential targets and PLK2 as a novel biomarker for the prognosis of human glioblastoma. PMID:35256538
Immune translational control by CPEB4 regulates intestinal inflammation resolution and colorectal cancer development. PMID:35243213
Overexpression of MUC1 Induces Non-Canonical TGF-β Signaling in Pancreatic Ductal Adenocarcinoma. PMID:35237602
Cancer proteogenomics: current impact and future prospects. PMID:35236940
Machine Learning-Based Analysis of Glioma Grades Reveals Co-Enrichment. PMID:35205761
PrimPol: A Breakthrough among DNA Replication Enzymes and a Potential New Target for Cancer Therapy. PMID:35204749
Novel Genetic Prognostic Signature for Lung Adenocarcinoma Identified by Differences in Gene Expression Profiles of Low- and High-Grade Histological Subtypes. PMID:35204661
PBK/TOPK Is a Favorable Prognostic Biomarker Correlated with Antitumor Immunity in Colon Cancers. PMID:35203508
Stage-differentiated ensemble modeling of DNA methylation landscapes uncovers salient biomarkers and prognostic signatures in colorectal cancer progression. PMID:35202405
Mutational signature profiling classifies subtypes of clinically different mismatch-repair-deficient tumours with a differential immunogenic response potential. PMID:35197584
Survival Genie, a web platform for survival analysis across pediatric and adult cancers. PMID:35197510
Cancer/Testis Antigen 55 is required for cancer cell proliferation and mitochondrial DNA maintenance. PMID:35189384
Design, Synthesis, and Biological Evaluation of Apcin-Based CDC20 Inhibitors. PMID:35178174
Potential Involvement of NSD1, KRT24 and ACACA in the Genetic Predisposition to Colorectal Cancer. PMID:35158968
Activation of PPARγ in bladder cancer via introduction of the long arm of human chromosome 9. PMID:35154423
Somatic mutational profiles and germline polygenic risk scores in human cancer. PMID:35144655
The ADAM9/UBN2/AKR1C3 axis promotes resistance to androgen-deprivation in prostate cancer. PMID:35141012
T cell receptors employ diverse strategies to target a p53 cancer neoantigen. PMID:35124005
Radiation therapy enhances immunotherapy response in microsatellite stable colorectal and pancreatic adenocarcinoma in a phase II trial. PMID:35122060
Pan-cancer computational histopathology reveals mutations, tumor composition and prognosis. PMID:35122049
Multi-omic analysis reveals significantly mutated genes and DDX3X as a sex-specific tumor suppressor in cutaneous melanoma. PMID:35121978
Negative trade-off between neoantigen repertoire breadth and the specificity of HLA-I molecules shapes antitumor immunity. PMID:35121862
Systematic evaluation of the prognostic and immunological role of PDLIM2 across 33 cancer types. PMID:35121770
A retrospective analysis of the correlation between AXL expression and clinical outcomes of patients with urothelial bladder carcinoma. PMID:35116837
Computational Prediction of the Pathogenic Status of Cancer-Specific Somatic Variants. PMID:35116056
Comparative assessment of genes driving cancer and somatic evolution in non-cancer tissues: an update of the Network of Cancer Genes (NCG) resource. PMID:35078504
Follicular Helper T-Cell-Based Classification of Endometrial Cancer Promotes Precise Checkpoint Immunotherapy and Provides Prognostic Stratification. PMID:35069566
Failure to Detect Mutations in U2AF1 due to Changes in the GRCh38 Reference Sequence. PMID:35041928
A lepidic gene signature predicts patient prognosis and sensitivity to immunotherapy in lung adenocarcinoma. PMID:35016696
Off-the-Shelf Prostate Stem Cell Antigen-Directed Chimeric Antigen Receptor Natural Killer Cell Therapy to Treat Pancreatic Cancer. PMID:34999097
Meta-analysis of whole-genome gene expression datasets assessing the effects of IDH1 and IDH2 mutations in isogenic disease models. PMID:34997121
Achieving robust somatic mutation detection with deep learning models derived from reference data sets of a cancer sample. PMID:34996510
Therapeutical interference with the epigenetic landscape of germ cell tumors: a comparative drug study and new mechanistical insights. PMID:34996497
The Estrogen Receptor α Signaling Pathway Controls Alternative Splicing in the Absence of Ligands in Breast Cancer Cells. PMID:34944881
Co-existing TP53 and ARID1A mutations promote aggressive endometrial tumorigenesis. PMID:34941867
Identification of α1,2-fucosylated signaling and adhesion molecules in head and neck squamous cell carcinoma. PMID:34939118
Subtype-Independent ANP32E Reduction During Breast Cancer Progression in Accordance with Chromatin Relaxation. PMID:34922480
ASO-Based PKM Splice-Switching Therapy Inhibits Hepatocellular Carcinoma Growth. PMID:34921016
KRAS mutation-independent downregulation of MAPK/PI3K signaling in colorectal cancer. PMID:34919787
Using a convolutional neural network for classification of squamous and non-squamous non-small cell lung cancer based on diagnostic histopathology HES images. PMID:34903781
Carboxypeptidase A1 (CPA1) Immunohistochemistry Is Highly Sensitive and Specific for Acinar Cell Carcinoma (ACC) of the Pancreas. PMID:34889867
Computational analysis of cancer genome sequencing data. PMID:34880424
Genetic and immunologic features of recurrent stage I lung adenocarcinoma. PMID:34880292
Identification of ferroptosis-related genes as potential biomarkers of tongue squamous cell carcinoma using an integrated bioinformatics approach. PMID:34878732
The iTHRIV Commons: a cross-institution information and health research data sharing architecture and web application. PMID:34850002
Epithelial Wnt secretion drives the progression of inflammation-induced colon carcinoma in murine model. PMID:34849464
Genetic and epigenetic regulation of the NRF2-KEAP1 pathway in human lung cancer. PMID:34845361
ELOVL2 promotes cancer progression by inhibiting cell apoptosis in renal cell carcinoma. PMID:34841437
Cell Cycle Regulation and DNA Damage Response Networks in Diffuse- and Intestinal-Type Gastric Cancer. PMID:34830941
Role of FRG1 in predicting the overall survivability in cancers using multivariate based optimal model. PMID:34795329
APOBEC Mutagenesis Inhibits Breast Cancer Growth through Induction of T cell-Mediated Antitumor Immune Responses. PMID:34795033
Identification of condition-specific biomarker systems in uterine cancer. PMID:34791179
Prediction and prognostic significance of ALOX12B and PACSIN1 expression in gastric cancer by genome-wide RNA expression and methylation analysis. PMID:34790376
Untangling the clinicopathological significance of MRE11-RAD50-NBS1 complex in sporadic breast cancers. PMID:34782604
QNBC Is Associated with High Genomic Instability Characterized by Copy Number Alterations and miRNA Deregulation. PMID:34768979
SMRT: Randomized Data Transformation for Cancer Subtyping and Big Data Analysis. PMID:34745946
Allele-specific genomic data elucidate the role of somatic gain and copy-number neutral loss of heterozygosity in cancer. PMID:34731645
The miRNA Profile of Inflammatory Colorectal Tumors Identify TGF-β as a Companion Target for Checkpoint Blockade Immunotherapy. PMID:34722540
Disease Modeling on Tumor Organoids Implicates AURKA as a Therapeutic Target in Liver Metastatic Colorectal Cancer. PMID:34700030
Identifying Complex lncRNA/Pseudogene-miRNA-mRNA Crosstalk in Hormone-Dependent Cancers. PMID:34681112
Convolutional neural network for human cancer types prediction by integrating protein interaction networks and omics data. PMID:34667236
Dysregulation of TFH-B-TRM lymphocyte cooperation is associated with unfavorable anti-PD-1 responses in EGFR-mutant lung cancer. PMID:34663810
The Landscape of the Tumor Microenvironment in Skin Cutaneous Melanoma Reveals a Prognostic and Immunotherapeutically Relevant Gene Signature. PMID:34660598
Therapeutic Effects of Inhibition of Sphingosine-1-Phosphate Signaling in HIF-2α Inhibitor-Resistant Clear Cell Renal Cell Carcinoma. PMID:34638286
Identification of an Immune-Related Long Noncoding RNA Pairs Model to Predict Survival and Immune Features in Gastric Cancer. PMID:34621744
DICER1 tumor predisposition syndrome: an evolving story initiated with the pleuropulmonary blastoma. PMID:34599283
Genomic Determinants of Homologous Recombination Deficiency across Human Cancers. PMID:34572800
Non-small-cell lung cancer classification via RNA-Seq and histology imaging probability fusion. PMID:34551733
Targeting non-canonical pathways as a strategy to modulate the sodium iodide symporter. PMID:34520744
Integrative Transcriptome-Wide Analyses Uncover Novel Risk-Associated MicroRNAs in Hormone-Dependent Cancers. PMID:34512726
Cancer-associated mutations in the p85α N-terminal SH2 domain activate a spectrum of receptor tyrosine kinases. PMID:34507989
The Cancer Epitope Database and Analysis Resource: A Blueprint for the Establishment of a New Bioinformatics Resource for Use by the Cancer Immunology Community. PMID:34504503
Mutation landscape of multiple myeloma measurable residual disease: identification of targets for precision medicine. PMID:34500459
The expressed mutational landscape of microsatellite stable colorectal cancers. PMID:34470667
DIANA-miTED: a microRNA tissue expression database. PMID:34469540
Transcriptional overlap links DNA hypomethylation with DNA hypermethylation at adjacent promoters in cancer. PMID:34462486
A Survey of Deep Learning for Lung Disease Detection on Medical Images: State-of-the-Art, Taxonomy, Issues and Future Directions. PMID:34460528
RP11-616M22.7 recapitulates imatinib resistance in gastrointestinal stromal tumor. PMID:34458010
MODEL-BASED FEATURE SELECTION AND CLUSTERING OF RNA-SEQ DATA FOR UNSUPERVISED SUBTYPE DISCOVERY. PMID:34457104
Fast mutual exclusivity algorithm nominates potential synthetic lethal gene pairs through brute force matrix product computations. PMID:34429855
The Oldest Co-opted gag Gene of a Human Endogenous Retrovirus Shows Placenta-Specific Expression and Is Upregulated in Diffuse Large B-Cell Lymphomas. PMID:34410386
Modeling the effects of EMT-immune dynamics on carcinoma disease progression. PMID:34408236
XOmiVAE: an interpretable deep learning model for cancer classification using high-dimensional omics data. PMID:34402865
Characterizing DNA methylation signatures and their potential functional roles in Merkel cell carcinoma. PMID:34399838
A systems-based framework to computationally describe putative transcription factors and signaling pathways regulating glycan biosynthesis. PMID:34367349
Pattern of placental alkaline phosphatase (PLAP) expression in human tumors: a tissue microarray study on 12,381 tumors. PMID:34363325
Low-Level Expression of MTUS1 Is Associated with Poor Survival in Patients with Lung Adenocarcinoma. PMID:34359333
Personalized Medicine in Ovarian Cancer: A Perspective From Mexico. PMID:34349852
Interaction with the CCT chaperonin complex limits APOBEC3A cytidine deaminase cytotoxicity. PMID:34347354
UCSCXenaShiny: An R/CRAN Package for Interactive Analysis of UCSC Xena Data. PMID:34323947
Filtering High-Dimensional Methylation Marks With Extremely Small Sample Size: An Application to Gastric Cancer Data. PMID:34322159
Reboot: a straightforward approach to identify genes and splicing isoforms associated with cancer patient prognosis. PMID:34316711
Aldo-Keto Reductases and Cancer Drug Resistance. PMID:34312303
A comprehensive analysis of SNPs and CNVs identifies novel markers associated with disease outcomes in colorectal cancer. PMID:34309201
Performance Comparisons of AlexNet and GoogLeNet in Cell Growth Inhibition IC50 Prediction. PMID:34299341
Inflammatory Cell Death, PANoptosis, Mediated by Cytokines in Diverse Cancer Lineages Inhibits Tumor Growth. PMID:34290111
Development of a Novel Immune Infiltration-Related ceRNA Network and Prognostic Model for Sarcoma. PMID:34277600
Prostasin regulates PD-L1 expression in human lung cancer cells. PMID:34240739
Oncogenic KRAS creates an aspartate metabolism signature in colorectal cancer cells. PMID:34227245
IGFBP2 Is a Potential Master Regulator Driving the Dysregulated Gene Network Responsible for Short Survival in Glioblastoma Multiforme. PMID:34211498
Germline ERBB2/HER2 Coding Variants Are Associated with Increased Risk of Myeloproliferative Neoplasms. PMID:34209587
OmiEmbed: A Unified Multi-Task Deep Learning Framework for Multi-Omics Data. PMID:34207255
Evaluation of Somatic Mutations in Solid Metastatic Pan-Cancer Patients. PMID:34204917
T-Cell Receptor Mimic Antibodies for Cancer Immunotherapy. PMID:34172530
Advancing targeted protein degradation for cancer therapy. PMID:34131295
Informatics Methods and Infrastructure Needed to Study Factors Associated with High Incidence of Pediatric Brain and Central Nervous System Tumors in Kentucky. PMID:34128919
Identification of lymphocyte cell-specific protein-tyrosine kinase (LCK) as a driver for invasion and migration of oral cancer by tumor heterogeneity exploitation. PMID:34116687
Using deep learning to identify bladder cancers with FGFR-activating mutations from histology images. PMID:34114376
Mammary cell gene expression atlas links epithelial cell remodeling events to breast carcinogenesis. PMID:34079055
Multi-Omics Model Applied to Cancer Genetics. PMID:34072237
Oncogenic Potential of the Dual-Function Protein MEX3A. PMID:34067172
Analysis and Interpretation of the Impact of Missense Variants in Cancer. PMID:34063805
Exonic variants undergoing allele-specific selection in cancers. PMID:34059054
Common pathways and functional profiles reveal underlying patterns in Breast, Kidney and Lung cancers. PMID:34039407
Differentiation-related zinc finger protein 750 suppresses cell growth in esophageal squamous cell carcinoma. PMID:33986873
Prediction of Synergistic Drug Combinations for Prostate Cancer by Transcriptomic and Network Characteristics. PMID:33986671
The genomic loci of specific human tRNA genes exhibit ageing-related DNA hypermethylation. PMID:33976121
Epigenetic dysregulation of immune-related pathways in cancer: bioinformatics tools and visualization. PMID:33963293
EBV miRNAs are potent effectors of tumor cell transcriptome remodeling in promoting immune escape. PMID:33956915
Environmental and sex-specific molecular signatures of glioma causation. PMID:33942853
Locus-Specific Characterization of Human Endogenous Retrovirus Expression in Prostate, Breast, and Colon Cancers. PMID:33941616
Opportunities and Challenges in Democratizing Immunology Datasets. PMID:33936065
BloodPAC Data Commons for Liquid Biopsy Data. PMID:33929890
Integrative reconstruction of cancer genome karyotypes using InfoGenomeR. PMID:33927198
PRKCA Overexpression Is Frequent in Young Oral Tongue Squamous Cell Carcinoma Patients and Is Associated with Poor Prognosis. PMID:33923093
Clinical Identification of Dysregulated Circulating microRNAs and Their Implication in Drug Response in Triple Negative Breast Cancer (TNBC) by Target Gene Network and Meta-Analysis. PMID:33918859
DPP9: Comprehensive In Silico Analyses of Loss of Function Gene Variants and Associated Gene Expression Signatures in Human Hepatocellular Carcinoma. PMID:33915844
Multi-Omics Analysis of Brain Metastasis Outcomes Following Craniotomy. PMID:33889540
Increased expression of peptides from non-coding genes in cancer proteomics datasets suggests potential tumor neoantigens. PMID:33888849
Identification of transcriptional subtypes in lung adenocarcinoma and squamous cell carcinoma through integrative analysis of microarray and RNA sequencing data. PMID:33888829
14q32 rearrangements deregulating BCL11B mark a distinct subgroup of T-lymphoid and myeloid immature acute leukemia. PMID:33876209
The Metabolic Landscape of RAS-Driven Cancers from biology to therapy. PMID:33870211
A Nomogram Combining a Four-Gene Biomarker and Clinical Factors for Predicting Survival of Melanoma. PMID:33868993
A deep learning model for the classification of indeterminate lung carcinoma in biopsy whole slide images. PMID:33854137
IGF2BP1, a Conserved Regulator of RNA Turnover in Cancer. PMID:33829040
Cost-effectiveness of Atezolizumab Plus Bevacizumab vs Sorafenib for Patients With Unresectable or Metastatic Hepatocellular Carcinoma. PMID:33825837
Breast Cancer Patient Prognosis Is Determined by the Interplay between TP53 Mutation and Alternative Transcript Expression: Insights from TP53 Long Amplicon Digital PCR Assays. PMID:33810361
TNMplot.com: A Web Tool for the Comparison of Gene Expression in Normal, Tumor and Metastatic Tissues. PMID:33807717
A Detailed Catalogue of Multi-Omics Methodologies for Identification of Putative Biomarkers and Causal Molecular Networks in Translational Cancer Research. PMID:33802234
The next horizon in precision oncology: Proteogenomics to inform cancer diagnosis and treatment. PMID:33798439
The Potential of hsa-mir-106b-5p as Liquid Biomarker in Prostate Cancer Patients in Indonesia. PMID:33773548
The human intermediate prolactin receptor is a mammary proto-oncogene. PMID:33772010
Identifying modules of cooperating cancer drivers. PMID:33769711
Accurate diagnosis of colorectal cancer based on histopathology images using artificial intelligence. PMID:33752648
DNA repair pathway activation features in follicular and papillary thyroid tumors, interrogated using 95 experimental RNA sequencing profiles. PMID:33748479
Targeting FAK in anticancer combination therapies. PMID:33731845
Integrated Characterization of lncRNA-Immune Interactions in Prostate Cancer. PMID:33665192
Pan-cancer investigation reveals mechanistic insights of planar cell polarity gene Fuz in carcinogenesis. PMID:33658400
Targeting a neoantigen derived from a common TP53 mutation. PMID:33649166
Construction and Analysis of Survival-Associated Competing Endogenous RNA Network in Lung Adenocarcinoma. PMID:33628780
Uniform genomic data analysis in the NCI Genomic Data Commons. PMID:33619257
Subcellular Localization of uc.8+ as a Prognostic Biomarker in Bladder Cancer Tissue. PMID:33567603
Simplified and Unified Access to Cancer Proteogenomic Data. PMID:33560848
Comprehensive characterization of protein-protein interactions perturbed by disease mutations. PMID:33558758
Inference of phenotype-relevant transcriptional regulatory networks elucidates cancer type-specific regulatory mechanisms in a pan-cancer study. PMID:33558504
MethCORR infers gene expression from DNA methylation and allows molecular analysis of ten common cancer types using fresh-frozen and formalin-fixed paraffin-embedded tumor samples. PMID:33509261
Online informatics resources to facilitate cancer target and chemical probe discovery. PMID:33479663
RNA splicing and aggregate gene expression differences in lung squamous cell carcinoma between patients of West African and European ancestry. PMID:33465699
Secondary Structural Model of MALAT1 Becomes Unstructured in Chronic Myeloid Leukemia and Undergoes Structural Rearrangement in Cervical Cancer. PMID:33450947
Aberrant splicing isoforms detected by full-length transcriptome sequencing as transcripts of potential neoantigens in non-small cell lung cancer. PMID:33397462
HeartBioPortal2.0: new developments and updates for genetic ancestry and cardiometabolic quantitative traits in diverse human populations. PMID:33382884
Molecular Network Profiling in Intestinal- and Diffuse-Type Gastric Cancer. PMID:33353109
The epigenetic regulator Mll1 is required for Wnt-driven intestinal tumorigenesis and cancer stemness. PMID:33349639
Cytoskeletal Control and Wnt Signaling-APC's Dual Contributions in Stem Cell Division and Colorectal Cancer. PMID:33348689
A Topic Modeling Analysis of TCGA Breast and Lung Cancer Transcriptomic Data. PMID:33339347
BaBao Dan Suppresses Tumor Growth of Pancreatic Cancer Through Modulating Transcriptional Reprogramming of Cancer-Related Genes. PMID:33330063
Regulatory T Cells Support Breast Cancer Progression by Opposing IFN-γ-Dependent Functional Reprogramming of Myeloid Cells. PMID:33296659
Cohesin mutations are synthetic lethal with stimulation of WNT signaling. PMID:33284104
Germline genomic patterns are associated with cancer risk, oncogenic pathways, and clinical outcomes. PMID:33246949
Intraoperative opioids are associated with improved recurrence-free survival in triple-negative breast cancer. PMID:33220939
canSAR: update to the cancer translational research and drug discovery knowledgebase. PMID:33219674
The Veterans Affairs Precision Oncology Data Repository, a Clinical, Genomic, and Imaging Research Database. PMID:33205130
The Clinical Kinase Index: A Method to Prioritize Understudied Kinases as Drug Targets for the Treatment of Cancer. PMID:33205077
Analysis of miR-9-5p, miR-124-3p, miR-21-5p, miR-138-5p, and miR-1-3p in Glioblastoma Cell Lines and Extracellular Vesicles. PMID:33187334
TCox: Correlation-Based Regularization Applied to Colorectal Cancer Survival Data. PMID:33182598
E-Cadherin, NFATC3, and PLP2 Are Differentially Methylated in Multiple Cancers. PMID:33178991
The tumor suppressor microRNA let-7 inhibits human LINE-1 retrotransposition. PMID:33177501
The M1/M2 spectrum and plasticity of malignant pleural effusion-macrophage in advanced lung cancer. PMID:33175182
Genomic Analysis of Vascular Invasion in HCC Reveals Molecular Drivers and Predictive Biomarkers. PMID:33140851
Functional analysis of low-grade glioma genetic variants predicts key target genes and transcription factors. PMID:33130899
The P72R Polymorphism in R248Q/W p53 Mutants Modifies the Mutant Effect on Epithelial to Mesenchymal Transition Phenotype and Cell Invasion via CXCL1 Expression. PMID:33126568
Multiomic Integration of Public Oncology Databases in Bioconductor. PMID:33119407
RUNX3 methylation drives hypoxia-induced cell proliferation and antiapoptosis in early tumorigenesis. PMID:33116296
Involvement of NEK2 and its interaction with NDC80 and CEP250 in hepatocellular carcinoma. PMID:33109182
RNA editing in cancer impacts mRNA abundance in immune response pathways. PMID:33106178
Why All the Fuss about Oxidative Phosphorylation (OXPHOS)? PMID:33103432
Dysregulated Expression and Methylation Analysis Identified TLX1NB as a Novel Recurrence Marker in Low-Grade Gliomas. PMID:33102572
FOXM1 drives HPV+ HNSCC sensitivity to WEE1 inhibition. PMID:33093209
The Dark Kinase Knowledgebase: an online compendium of knowledge and experimental results of understudied kinases. PMID:33079988
Guanosine triphosphate links MYC-dependent metabolic and ribosome programs in small-cell lung cancer. PMID:33079728
PopInf: An Approach for Reproducibly Visualizing and Assigning Population Affiliation in Genomic Samples of Uncertain Origin. PMID:33074720
Pan-cancer driver copy number alterations identified by joint expression/CNA data analysis. PMID:33057153
Present and Future of Anti-Glioblastoma Therapies: A Deep Look into Molecular Dependencies/Features. PMID:33053763
iMOKA: k-mer based software to analyze large collections of sequencing data. PMID:33050927
Target Enrichment Enables the Discovery of lncRNAs with Somatic Mutations or Altered Expression in Paraffin-Embedded Colorectal Cancer Samples. PMID:33019720
Germline and somatic albinism variants in amelanotic/hypomelanotic melanoma: Increased carriage of TYR and OCA2 variants. PMID:32966289
MicroRNA-Related Prognosis Biomarkers from High-Throughput Sequencing Data of Colorectal Cancer. PMID:32964043
Matching cell lines with cancer type and subtype of origin via mutational, epigenomic, and transcriptomic patterns. PMID:32937430
Deep learning based feature-level integration of multi-omics data for breast cancer patients survival analysis. PMID:32933515
Evolutionary dynamics of neoantigens in growing tumors. PMID:32929288
Identification of Biomarkers to Construct a Competing Endogenous RNA Network and Establishment of a Genomic-Clinicopathologic Nomogram to Predict Survival for Children with Rhabdoid Tumors of the Kidney. PMID:32908900
Improving Model Performance on the Stratification of Breast Cancer Patients by Integrating Multiscale Genomic Features. PMID:32908867
Identification of a novel subgroup of endometrial cancer patients with loss of thyroid hormone receptor beta expression and improved survival. PMID:32894083
High expression of MKK3 is associated with worse clinical outcomes in African American breast cancer patients. PMID:32873298
Human Endogenous Retrovirus Expression Is Associated with Head and Neck Cancer and Differential Survival. PMID:32872377
HPV-EM: an accurate HPV detection and genotyping EM algorithm. PMID:32868873
Co-expression analysis of pancreatic cancer proteome reveals biology and prognostic biomarkers. PMID:32860207
Profilin choreographs actin and microtubules in cells and cancer. PMID:32859370
Pan-Cancer Classification Based on Self-Normalizing Neural Networks and Feature Selection. PMID:32850695
Genomic and epigenetic aberrations of chromosome 1p36.13 have prognostic implications in malignancies. PMID:32816122
ABC-GWAS: Functional Annotation of Estrogen Receptor-Positive Breast Cancer Genetic Variants. PMID:32765587
The Ubiquitin Ligase TRIP12 Limits PARP1 Trapping and Constrains PARP Inhibitor Efficiency. PMID:32755579
Tousled-Like Kinases Suppress Innate Immune Signaling Triggered by Alternative Lengthening of Telomeres. PMID:32755577
AGR3 promotes estrogen receptor-positive breast cancer cell proliferation in an estrogen-dependent manner. PMID:32724387
PertInInt: An Integrative, Analytical Approach to Rapidly Uncover Cancer Driver Genes with Perturbed Interactions and Functionalities. PMID:32711844
Infiltrative tumour growth pattern correlates with poor outcome in oesophageal cancer. PMID:32675198
A redox-active switch in fructosamine-3-kinases expands the regulatory repertoire of the protein kinase superfamily. PMID:32636308
Efficient weighted univariate clustering maps outstanding dysregulated genomic zones in human cancers. PMID:32619008
Seq-ing answers: Current data integration approaches to uncover mechanisms of transcriptional regulation. PMID:32612756
Dysregulation of MITF Leads to Transformation in MC1R-Defective Melanocytes. PMID:32605315
A Translational Pipeline for Overall Survival Prediction of Breast Cancer Patients by Decision-Level Integration of Multi-Omics Data. PMID:32601549
Wnt-driven LARGE2 mediates laminin-adhesive O-glycosylation in human colonic epithelial cells and colorectal cancer. PMID:32586342
Weakly-supervised learning for lung carcinoma classification using deep learning. PMID:32518413
Oncogenic Gene-Expression Programs in Leiomyosarcoma and Characterization of Conventional, Inflammatory, and Uterogenic Subtypes. PMID:32518213
Whole-genome sequencing of glioblastoma reveals enrichment of non-coding constraint mutations in known and novel genes. PMID:32513296
DSCAM-AS1-Driven Proliferation of Breast Cancer Cells Involves Regulation of Alternative Exon Splicing and 3'-End Usage. PMID:32503257
Bioinformatics Analysis based on Multiple Databases Identifies Hub Genes Associated with Hepatocellular Carcinoma. PMID:32476992
Immunoscore Predicts Survival in Early-Stage Lung Adenocarcinoma Patients. PMID:32457841
CVCDAP: an integrated platform for molecular and clinical analysis of cancer virtual cohorts. PMID:32449936
Visualizing and interpreting cancer genomics data via the Xena platform. PMID:32444850
Multi-omic signatures identify pan-cancer classes of tumors beyond tissue of origin. PMID:32433524
Germline variant burden in cancer genes correlates with age at diagnosis and somatic mutation burden. PMID:32415133
Gene networks and expression quantitative trait loci associated with adjuvant chemotherapy response in high-grade serous ovarian cancer. PMID:32404140
RNA Sequencing in Comparison to Immunohistochemistry for Measuring Cancer Biomarkers in Breast Cancer and Lung Cancer Specimens. PMID:32397474
MAPK pathway mutations in head and neck cancer affect immune microenvironments and ErbB3 signaling. PMID:32381551
Genome-Scale Metabolic Modeling of Glioblastoma Reveals Promising Targets for Drug Development. PMID:32362913
Mutational signatures are jointly shaped by DNA damage and repair. PMID:32358516
The Exceptional Responders Initiative: Feasibility of a National Cancer Institute Pilot Study. PMID:32339229
MethCORR modelling of methylomes from formalin-fixed paraffin-embedded tissue enables characterization and prognostication of colorectal cancer. PMID:32332866
High-throughput gene screen reveals modulators of nuclear shape. PMID:32320319
Computational Oncology in the Multi-Omics Era: State of the Art. PMID:32318338
PDZ Domains as Drug Targets. PMID:32313833
Identification of a RAS-activating TMEM87A-RASGRF1 Fusion in an Exceptional Responder to Sunitinib with Non-Small Cell Lung Cancer. PMID:32312893
Developing Real-world Evidence-Ready Datasets: Time for Clinician Engagement. PMID:32297007
Molecular effects of dADD1 misexpression in chromatin organization and transcription. PMID:32293240
Computing Skin Cutaneous Melanoma Outcome From the HLA-Alleles and Clinical Characteristics. PMID:32273881
SAMHD1 Functions and Human Diseases. PMID:32244340
Phenotypic Screening of Chemical Libraries Enriched by Molecular Docking to Multiple Targets Selected from Glioblastoma Genomic Data. PMID:32243127
Convolutional neural network models for cancer type prediction based on gene expression. PMID:32241303
Extracellular Protease ADAMTS1 Is Required at Early Stages of Human Uveal Melanoma Development by Inducing Stemness and Endothelial-Like Features on Tumor Cells. PMID:32230715
ecTMB: a robust method to estimate and classify tumor mutational burden. PMID:32188929
Gene mutations distinguishing gastric from colorectal and esophageal adenocarcinomas. PMID:32175104
Ensemble disease gene prediction by clinical sample-based networks. PMID:32164526
Leptomeningeal Metastasis from Adrenocortical Carcinoma: A Case Report. PMID:32154490
CancerLivER: a database of liver cancer gene expression resources and biomarkers. PMID:32147717
Impact of a deep learning assistant on the histopathologic classification of liver cancer. PMID:32140566
Mutations in the coat complex II component SEC23B promote colorectal cancer metastasis. PMID:32123160
Cell-free DNA analysis reveals POLR1D-mediated resistance to bevacizumab in colorectal cancer. PMID:32087735
Pathway-guided analysis identifies Myc-dependent alternative pre-mRNA splicing in aggressive prostate cancers. PMID:32086391
Integrative analysis of breast cancer profiles in TCGA by TNBC subgrouping reveals novel microRNA-specific clusters, including miR-17-92a, distinguishing basal-like 1 and basal-like 2 TNBC subtypes. PMID:32085745
Variability in estimated gene expression among commonly used RNA-seq pipelines. PMID:32066774
Proteogenomic Characterization of Endometrial Carcinoma. PMID:32059776
MAL2-Induced Actin-Based Protrusion Formation is Anti-Oncogenic in Hepatocellular Carcinoma. PMID:32059473
Low expression of pro-apoptotic proteins Bax, Bak and Smac indicates prolonged progression-free survival in chemotherapy-treated metastatic melanoma. PMID:32054850
Combined burden and functional impact tests for cancer driver discovery using DriverPower. PMID:32024818
decorate: differential epigenetic correlation test. PMID:32003784
Preclinical evaluation of an affinity-enhanced MAGE-A4-specific T-cell receptor for adoptive T-cell therapy. PMID:32002290
Deep Learning Models for Histopathological Classification of Gastric and Colonic Epithelial Tumours. PMID:32001752
Identification of Platform-Independent Diagnostic Biomarker Panel for Hepatocellular Carcinoma Using Large-Scale Transcriptomics Data. PMID:31998366
Clinical Genome Data Model (cGDM) provides Interactive Clinical Decision Support for Precision Medicine. PMID:31996707
A deep learning image-based intrinsic molecular subtype classifier of breast tumors reveals tumor heterogeneity that may affect survival. PMID:31992350
Choice of library size normalization and statistical methods for differential gene expression analysis in balanced two-group comparisons for RNA-seq studies. PMID:31992223
Knowledge-guided analysis of "omics" data using the KnowEnG cloud platform. PMID:31971940
Tissue-guided LASSO for prediction of clinical drug response using preclinical samples. PMID:31967990
Extreme intratumour heterogeneity and driver evolution in mismatch repair deficient gastro-oesophageal cancer. PMID:31949146
Progesterone Receptor Gene Variants in Metastatic Estrogen Receptor Positive Breast Cancer. PMID:31942683
CNApp, a tool for the quantification of copy number alterations and integrative analysis revealing clinical implications. PMID:31939734
TP63 isoform expression is linked with distinct clinical outcomes in cancer. PMID:31927310
A Strong Decrease in TIMP3 Expression Mediated by the Presence of miR-17 and 20a Enables Extracellular Matrix Remodeling in the NSCLC Lesion Surroundings. PMID:31921636
Novel Breast-Specific Long Non-coding RNA LINC00993 Acts as a Tumor Suppressor in Triple-Negative Breast Cancer. PMID:31921620
LINC01714 Enhances Gemcitabine Sensitivity by Modulating FOXO3 Phosphorylation in Cholangiocarcinoma. PMID:31902744
CaSpER identifies and visualizes CNV events by integrative analysis of single-cell or bulk RNA-sequencing data. PMID:31900397
Monitoring methylation-driven genes as prognostic biomarkers in patients with lung squamous cell cancer. PMID:31897186
An ancestry informative marker panel design for individual ancestry estimation of Hispanic population using whole exome sequencing data. PMID:31888480
Immunohistochemical Analysis Revealed a Correlation between Musashi-2 and Cyclin-D1 Expression in Patients with Oral Squamous Cells Carcinoma. PMID:31878037
iMIRAGE: an R package to impute microRNA expression using protein-coding genes. PMID:31860075
Differential alternative splicing regulation among hepatocellular carcinoma with different risk factors. PMID:31856847
FIREVAT: finding reliable variants without artifacts in human cancer samples using etiologically relevant mutational signatures. PMID:31847917
MeinteR: A framework to prioritize DNA methylation aberrations based on conformational and cis-regulatory element enrichment. PMID:31844073
Platform-integrated mRNA isoform quantification. PMID:31834359
Comprehensive Identification and Characterization of Human Secretome Based on Integrative Proteomic and Transcriptomic Data. PMID:31824949
GenoSurf: metadata driven semantic search system for integrated genomic datasets. PMID:31820804
Pannexin1 Is Associated with Enhanced Epithelial-To-Mesenchymal Transition in Human Patient Breast Cancer Tissues and in Breast Cancer Cell Lines. PMID:31817827
Cardioinformatics: the nexus of bioinformatics and precision cardiology. PMID:31802103
Improving survival prediction using a novel feature selection and feature reduction framework based on the integration of clinical and molecular data. PMID:31797615
Identification and ranking of recurrent neo-epitopes in cancer. PMID:31775766
Computational Inference of Gene Co-Expression Networks for the identification of Lung Carcinoma Biomarkers: An Ensemble Approach. PMID:31766738
Common polymorphic inversions at 17q21.31 and 8p23.1 associate with cancer prognosis. PMID:31753042
Multiplatform biomarker identification using a data-driven approach enables single-sample classification. PMID:31752658
Cross-Talk Between circRNAs and mRNAs Modulates MiRNA-mediated Circuits and Affects Melanoma Plasticity. PMID:31734859
Pan-cancer clinical and molecular analysis of racial disparities. PMID:31730714
Secondary Structural Model of Human MALAT1 Reveals Multiple Structure-Function Relationships. PMID:31717552
DeePathology: Deep Multi-Task Learning for Inferring Molecular Pathology from Cancer Transcriptome. PMID:31712594
Impact of mouse contamination in genomic profiling of patient-derived models and best practice for robust analysis. PMID:31707992
Replication timing alterations in leukemia affect clinically relevant chromosome domains. PMID:31698451
TYK2: An Upstream Kinase of STATs in Cancer. PMID:31694222
UCSC Genome Browser enters 20th year. PMID:31691824
The Many Faces of Gene Regulation in Cancer: A Computational Oncogenomics Outlook. PMID:31671657
Functional analysis of RPS27 mutations and expression in melanoma. PMID:31663663
The impact of nonsense-mediated mRNA decay on genetic disease, gene editing and cancer immunotherapy. PMID:31659324
Distinct molecular etiologies of male and female hepatocellular carcinoma. PMID:31615477
Illuminating biological pathways for drug targeting in head and neck squamous cell carcinoma. PMID:31596908
Loss of Janus Associated Kinase 1 Alters Urothelial Cell Function and Facilitates the Development of Bladder Cancer. PMID:31552026
In Silico Drug Prescription for Targeting Cancer Patient Heterogeneity and Prediction of Clinical Outcome. PMID:31540260
Nuclear control of lung cancer cells migration, invasion and bioenergetics by eukaryotic translation initiation factor 3F. PMID:31527668
Big Data and Artificial Intelligence Modeling for Drug Discovery. PMID:31518513
Are screening methods useful in feature selection? An empirical study. PMID:31509541
The Cancer-Associated Genetic Variant Rs3903072 Modulates Immune Cells in the Tumor Microenvironment. PMID:31507631
Inclusiveness and ethical considerations for observational, translational, and clinical cancer health disparity research. PMID:31502259
Single-cell transcriptomics reveals multi-step adaptations to endocrine therapy. PMID:31477698
CCN1 interlinks integrin and hippo pathway to autoregulate tip cell activity. PMID:31429823
Integrated systems-genetic analyses reveal a network target for delaying glioma progression. PMID:31420939
ARID1A and PI3-kinase pathway mutations in the endometrium drive epithelial transdifferentiation and collective invasion. PMID:31391455
Substantial batch effects in TCGA exome sequences undermine pan-cancer analysis of germline variants. PMID:31391007
CpG promoter hypo-methylation and up-regulation of microRNA-190b in hormone receptor-positive breast cancer. PMID:31384394
DNMT3A co-mutation in an IDH1-mutant glioblastoma. PMID:31371348
A plea for taking all available clinical information into account when assessing the predictive value of omics data. PMID:31340753
In Silico Analysis of Gene Expression Change Associated with Copy Number of Enhancers in Pancreatic Adenocarcinoma. PMID:31336658
Quantifying gene selection in cancer through protein functional alteration bias. PMID:31334812
Association of imputed prostate cancer transcriptome with disease risk reveals novel mechanisms. PMID:31308362
HeartBioPortal. PMID:31294639
Correlation Analysis of Histopathology and Proteogenomics Data for Breast Cancer. PMID:31285282
Reproducibility and Transparency by Design. PMID:31273047
Implementing the FAIR Data Principles in precision oncology: review of supporting initiatives. PMID:31263868
Insights into Impact of DNA Copy Number Alteration and Methylation on the Proteogenomic Landscape of Human Ovarian Cancer via a Multi-omics Integrative Analysis. PMID:31227599
Off-label use of common predictive biomarkers in gastrointestinal malignancies: a critical appraisal. PMID:31221175
Machine learning with the TCGA-HNSC dataset: improving usability by addressing inconsistency, sparsity, and high-dimensionality. PMID:31208324
ATR mediates cisplatin resistance in 3D-cultured breast cancer cells via translesion DNA synthesis modulation. PMID:31189884
An overview of publicly available patient-centered prostate cancer datasets. PMID:31143673
Associating somatic mutations to clinical outcomes: a pan-cancer study of survival time. PMID:31138328
Rare variant phasing using paired tumor:normal sequence data. PMID:31132991
Kremen1-induced cell death is regulated by homo- and heterodimerization. PMID:31069116
SpliceV: analysis and publication quality printing of linear and circular RNA splicing, expression and regulation. PMID:31068132
ClinOmicsTrailbc: a visual analytics tool for breast cancer treatment stratification. PMID:31038669
PseudoFuN: Deriving functional potentials of pseudogenes from integrative relationships with genes and microRNAs across 32 cancers. PMID:31029062
NAD metabolic dependency in cancer is shaped by gene amplification and enhancer remodelling. PMID:31019297
Expression Profiling of Calcium Channels and Calcium-Activated Potassium Channels in Colorectal Cancer. PMID:31010205
A novel CRISPR-engineered prostate cancer cell line defines the AR-V transcriptome and identifies PARP inhibitor sensitivities. PMID:31006810
Platform-Independent Classification System to Predict Molecular Subtypes of High-Grade Serous Ovarian Carcinoma. PMID:31002564
Insights into rheumatic diseases from next-generation sequencing. PMID:31000790
Reproducible big data science: A case study in continuous FAIRness. PMID:30973881
Shallow Sparsely-Connected Autoencoders for Gene Set Projection. PMID:30963076
Integrated Somatic and Germline Whole-Exome Sequencing Analysis in Women with Lung Cancer after a Previous Breast Cancer. PMID:30925779
NOJAH: NOt Just Another Heatmap for genome-wide cluster analysis. PMID:30921318
Tumorigenesis as the Paradigm of Quasi-neutral Molecular Evolution. PMID:30912799
TACCO, a Database Connecting Transcriptome Alterations, Pathway Alterations and Clinical Outcomes in Cancers. PMID:30846808
Recurrence analysis on prostate cancer patients with Gleason score 7 using integrated histopathology whole-slide images and genomic data through deep neural networks. PMID:30840742
CDK7 inhibition as a promising therapeutic strategy for lung squamous cell carcinomas with a SOX2 amplification. PMID:30838525
Deep convolutional neural networks for accurate somatic mutation detection. PMID:30833567
Exceptional response and multisystem autoimmune-like toxicities associated with the same T cell clone in a patient with uveal melanoma treated with immune checkpoint inhibitors. PMID:30832716
Histone 4 Lysine 20 Methylation: A Case for Neurodevelopmental Disease. PMID:30832413
Clinical and research applications of a brain tumor tissue bank in the age of precision medicine. PMID:30816054
Correlation Patterns Between DNA Methylation and Gene Expression in The Cancer Genome Atlas. PMID:30792573
Small RNA expression from viruses, bacteria and human miRNAs in colon cancer tissue and its association with microsatellite instability and tumor location. PMID:30786859
In silico analysis reveals a shared immune signature in CASP8-mutated carcinomas with varying correlations to prognosis. PMID:30775178
deepDriver: Predicting Cancer Driver Genes Based on Somatic Mutations Using Deep Convolutional Neural Networks. PMID:30761181
A scalable, aggregated genotypic-phenotypic database for human disease variation. PMID:30759220
Inhibition of oncogenic Src induces FABP4-mediated lipolysis via PPARγ activation exerting cancer growth suppression. PMID:30755372
Neoadjuvant anti-PD-1 immunotherapy promotes a survival benefit with intratumoral and systemic immune responses in recurrent glioblastoma. PMID:30742122
Modeling double strand break susceptibility to interrogate structural variation in cancer. PMID:30736820
Data Lakes, Clouds, and Commons: A Review of Platforms for Analyzing and Sharing Genomic Data. PMID:30691868
Robust in-silico identification of Cancer Cell Lines based on RNA and targeted DNA sequencing data. PMID:30674903
A recurrent cancer-associated substitution in DNA polymerase ε produces a hyperactive enzyme. PMID:30670691
Desmoglein 1 Regulates Invadopodia by Suppressing EGFR/Erk Signaling in an Erbin-Dependent Manner. PMID:30655320
APOBEC-induced mutations and their cancer effect size in head and neck squamous cell carcinoma. PMID:30647454
Characterization of heterogeneous redox responses in hepatocellular carcinoma patients using network analysis. PMID:30606699
Exploring the differences between early-onset gastric cancer and traditional-onset gastric cancer. PMID:30603136
Model based on GA and DNN for prediction of mRNA-Smad7 expression regulated by miRNAs in breast cancer. PMID:30594253
Comparative proteogenomic analysis of right-sided colon cancer, left-sided colon cancer and rectal cancer reveals distinct mutational profiles. PMID:30577807
Power in pairs: assessing the statistical value of paired samples in tests for differential expression. PMID:30572829
TriPOINT: a software tool to prioritize important genes in pathways and their non-coding regulators. PMID:30566622
Identification and characterization of an alternative cancer-derived PD-L1 splice variant. PMID:30564890
Systematic domain-based aggregation of protein structures highlights DNA-, RNA- and other ligand-binding positions. PMID:30535108
Interpretation of an individual functional genomics experiment guided by massive public data. PMID:30478325
Analysis of 7,815 cancer exomes reveals associations between mutational processes and somatic driver mutations. PMID:30412573
PreMedKB: an integrated precision medicine knowledgebase for interpreting relationships between diseases, genes, variants and drugs. PMID:30407536
Enabling precision medicine in neonatology, an integrated repository for preterm birth research. PMID:30398470
Effect Sizes of Somatic Mutations in Cancer. PMID:30365005
ELMER v.2: an R/Bioconductor package to reconstruct gene regulatory networks from DNA methylation and transcriptome profiles. PMID:30364927
Identification and validation of a tumor-infiltrating Treg transcriptional signature conserved across species and tumor types. PMID:30348759
Implications of Epigenetic Drift in Colorectal Neoplasia. PMID:30291105
A group of long noncoding RNAs identified by data mining can predict the prognosis of lung adenocarcinoma. PMID:30290038
Using Semantic Web Technologies to Enable Cancer Genomics Discovery at Petabyte Scale. PMID:30283230
Structure and evolution of double minutes in diagnosis and relapse brain tumors. PMID:30267146
Exome-wide analysis of bi-allelic alterations identifies a Lynch phenotype in The Cancer Genome Atlas. PMID:30217226
A TOP2A-derived cancer panel drives cancer progression in papillary renal cell carcinoma. PMID:30214555
Cancer expression quantitative trait loci (eQTLs) can be determined from heterogeneous tumor gene expression data by modeling variation in tumor purity. PMID:30205839
SequencEnG: an interactive knowledge base of sequencing techniques. PMID:30202870
Genetic Predisposition to Neuroblastoma. PMID:30200332
Copy Number Alterations in Tumor Genomes Deleting Antineoplastic Drug Targets Partially Compensated by Complementary Amplifications. PMID:30194077
Systematic analysis reveals molecular characteristics of ERG-negative prostate cancer. PMID:30150711
From hype to reality: data science enabling personalized medicine. PMID:30145981
Dissecting the expression landscape of mitochondrial genes in lung squamous cell carcinoma and lung adenocarcinoma. PMID:30128019
South Korea: in the midst of a privacy reform centered on data sharing. PMID:30121900
Endogenous HIF2A reporter systems for high-throughput functional screening. PMID:30104738
Pan-Cancer Analysis Reveals Differential Susceptibility of Bidirectional Gene Promoters to DNA Methylation, Somatic Mutations, and Copy Number Alterations. PMID:30081598
Aberrant DNMT3B7 expression correlates to tissue type, stage, and survival across cancers. PMID:30071066
Metabolic Network-Based Identification and Prioritization of Anticancer Targets Based on Expression Data in Hepatocellular Carcinoma. PMID:30065658
Cancerin: A computational pipeline to infer cancer-associated ceRNA interaction networks. PMID:30011266
S100A10, a novel biomarker in pancreatic ductal adenocarcinoma. PMID:30009399
Copy number profiling across glioblastoma populations has implications for clinical trial design. PMID:29982740
Differential Integration of Transcriptome and Proteome Identifies Pan-Cancer Prognostic Biomarkers. PMID:29971090
An antisense RNA capable of modulating the expression of the tumor suppressor microRNA-34a. PMID:29970884
Consensus molecular subtype classification of colorectal adenomas. PMID:29968252
iReceptor: A platform for querying and analyzing antibody/B-cell and T-cell receptor repertoire data across federated repositories. PMID:29944754
Cloud computing applications for biomedical science: A perspective. PMID:29902176
Chromatic: WebAssembly-Based Cancer Genome Viewer. PMID:29881254
MicroRNA-Related Genetic Variants Associated with Survival of Head and Neck Squamous Cell Carcinoma. PMID:29880533
Changing Trends in Computational Drug Repositioning. PMID:29874824
The National Sleep Research Resource: towards a sleep data commons. PMID:29860441
Landscape of Microsatellite Instability Across 39 Cancer Types. PMID:29850653
Progress Toward Cancer Data Ecosystems. PMID:29794537
Credentialing Individual Samples for Proteogenomic Analysis. PMID:29716986
Estimation of the Percentage of US Patients With Cancer Who Benefit From Genome-Driven Oncology. PMID:29710180
Community-driven roadmap for integrated disease maps. PMID:29688273
CDKN2A Copy Number Loss Is an Independent Prognostic Factor in HPV-Negative Head and Neck Squamous Cell Carcinoma. PMID:29670856
PRDM4 mediates YAP-induced cell invasion by activating leukocyte-specific integrin β2 expression. PMID:29669796
A p53/miR-30a/ZEB2 axis controls triple negative breast cancer aggressiveness. PMID:29666469
SLAM-seq defines direct gene-regulatory functions of the BRD4-MYC axis. PMID:29622725
Finding cancer driver mutations in the era of big data research. PMID:29611034
T cell receptor-β J usage, in combination with particular HLA class II alleles, correlates with better cancer survival rates. PMID:29594966
SRARP and HSPB7 are epigenetically regulated gene pairs that function as tumor suppressors and predict clinical outcome in malignancies. PMID:29577611
Differential expression and prognostic value of long non-coding RNA in HPV-negative head and neck squamous cell carcinoma. PMID:29575229
Ensemble Methods with Voting Protocols Exhibit Superior Performance for Predicting Cancer Clinical Endpoints and Providing More Complete Coverage of Disease-Related Genes. PMID:29546047
The absence of a novel intron 19-retaining ALK transcript (ALK-I19) and MYCN amplification correlates with an excellent clinical outcome in neuroblastoma patients. PMID:29535836
The evolutionary pattern of mutations in glioblastoma reveals therapy-mediated selection. PMID:29487696
A common molecular signature of intestinal-type gastric carcinoma indicates processes related to gastric carcinogenesis. PMID:29484116
Heterogeneity and mutation in KRAS and associated oncogenes: evaluating the potential for the evolution of resistance to targeting of KRAS G12C. PMID:29453361
Dexamethasone-Mediated Upregulation of Calreticulin Inhibits Primary Human Glioblastoma Dispersal Ex Vivo. PMID:29443896
Liquid biopsy and its role in an advanced clinical trial for lung cancer. PMID:29405770
Loss-of-function uORF mutations in human malignancies. PMID:29402903
Mortality, morbidity and health in developed societies: a review of data sources. PMID:29398718
Functional Analysis of Cancer-Associated DNA Polymerase ε Variants in Saccharomyces cerevisiae. PMID:29352080
Integrative Genomic Analysis Predicts Causative Cis-Regulatory Mechanisms of the Breast Cancer-Associated Genetic Variant rs4415084. PMID:29351903
Isocitrate dehydrogenase 1 mutation subtypes at site 132 and their translational potential in glioma. PMID:29303363
Scalable non-negative matrix tri-factorization. PMID:29299064
Cancer transcriptome profiling at the juncture of clinical translation. PMID:29279605
The ubiquitous 'cancer mutational signature' 5 occurs specifically in cancers with deleted FHIT alleles. PMID:29254236
Informatics for cancer immunotherapy. PMID:29253114
Accelerating Discovery of Functional Mutant Alleles in Cancer. PMID:29247016
Breast cancer: The translation of big genomic data to cancer precision medicine. PMID:29215763
Epigenetic regulation of AXL and risk of childhood asthma symptoms. PMID:29177020
Computational biologists: moving to the driver's seat. PMID:29169371
Matrix Metalloproteinases Polymorphisms as Prognostic Biomarkers in Malignant Pleural Mesothelioma. PMID:29138529
Availability and Use of Shared Data From Cardiometabolic Clinical Trials. PMID:29133600
Statistical Contributions to Bioinformatics: Design, Modeling, Structure Learning, and Integration. PMID:29129969
Systematically linking tranSMART, Galaxy and EGA for reusing human translational research data. PMID:29123641
Comprehensive Characterization of Alternative Polyadenylation in Human Cancer. PMID:29106591
Developing Cancer Informatics Applications and Tools Using the NCI Genomic Data Commons API. PMID:29092930
An Assessment of Imaging Informatics for Precision Medicine in Cancer. PMID:29063549
SBCDDB: Sleeping Beauty Cancer Driver Database for gene discovery in mouse models of human cancers. PMID:29059366
Identification of a key role of widespread epigenetic drift in Barrett's esophagus and esophageal adenocarcinoma. PMID:29046735
A Comprehensive Infrastructure for Big Data in Cancer Research: Accelerating Cancer Research and Precision Medicine. PMID:28983483
Resources for Interpreting Variants in Precision Genomic Oncology Applications. PMID:28975082
Pathway-Enriched Gene Signature Associated with 53BP1 Response to PARP Inhibition in Triple-Negative Breast Cancer. PMID:28958991
C1orf64 is a novel androgen receptor target gene and coregulator that interacts with 14-3-3 protein in breast cancer. PMID:28915724
Lower frequency of TLR9 variant associated with protection from breast cancer among African Americans. PMID:28886076
Molecular signatures that can be transferred across different omics platforms. PMID:28881975
Frizzled-5: a high affinity receptor for secreted frizzled-related protein-2 activation of nuclear factor of activated T-cells c3 signaling to promote angiogenesis. PMID:28840375
Uncovering robust patterns of microRNA co-expression across cancers using Bayesian Relevance Networks. PMID:28817636
EINCR1 is an EGF inducible lincRNA overexpressed in lung adenocarcinomas. PMID:28732076
Cytosine Deaminase APOBEC3A Sensitizes Leukemia Cells to Inhibition of the DNA Replication Checkpoint. PMID:28655787
Perspective on Precision Medicine in Oncology. PMID:28632968
Pan-cancer analysis reveals technical artifacts in TCGA germline variant calls. PMID:28606096
AACR Project GENIE: Powering Precision Medicine through an International Consortium. PMID:28572459
Multidimensional scaling of diffuse gliomas: application to the 2016 World Health Organization classification system with prognostically relevant molecular subtype discovery. PMID:28532485
MET Exon 14 Mutation Encodes an Actionable Therapeutic Target in Lung Adenocarcinoma. PMID:28522754
From Rosalind Franklin to Barack Obama: Data Sharing Challenges and Solutions in Genomics and Personalised Medicine. PMID:28517986
Diffuse large B-cell lymphoma: can genomics improve treatment options for a curable cancer? PMID:28487884
Bioinformatics in translational drug discovery. PMID:28487472
Towards a global cancer knowledge network: dissecting the current international cancer genomic sequencing landscape. PMID:28453708
Comprehensive discovery of subsample gene expression components by information explanation: therapeutic implications in cancer. PMID:28292312
Collaborating to Compete: Blood Profiling Atlas in Cancer (BloodPAC) Consortium. PMID:28187516
Implementing Genome-Driven Oncology. PMID:28187282
Genomics pipelines and data integration: challenges and opportunities in the research setting. PMID:28092471
The 21st Century Cures Act - A View from the NIH. PMID:27959585
Approaches to modernize the combination drug development paradigm. PMID:27793177
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cancer
metasource: Fairsharing.org
version: FAIRsharing.org: NCI GDC; National Cancer Institute's Genomic Data Commons; DOI: https://doi.org/10.25504/FAIRsharing.RyVjoS; Last edited: July 31, 2020, 2:04 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
Tags
More detailed information about this field from each metasource.
cancer
metasource: Fairsharing.orgversion: FAIRsharing.org: NCI GDC; National Cancer Institute's Genomic Data Commons; DOI: https://doi.org/10.25504/FAIRsharing.RyVjoS; Last edited: July 31, 2020, 2:04 p.m.; Last accessed: Jan 03 2022 7:06 p.m.
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